Record git-annex (5.20131127) in archive suite sid

639 files changed, 11154 insertions, 1839 deletions

diff --git a/.gitattributes b/.gitattributes
deleted file mode 100644
index 5d425843f..000000000
--- a/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-debian/changelog merge=dpkg-mergechangelogs
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 221087847..000000000
--- a/.gitignore
+++ /dev/null
@@ -1,31 +0,0 @@
-tags
-Setup
-*.hi
-*.o
-tmp
-test
-build-stamp
-Build/SysConfig.hs
-Build/InstallDesktopFile
-Build/EvilSplicer
-Build/Standalone
-Build/OSXMkLibs
-git-annex
-git-annex.1
-git-annex-shell.1
-git-union-merge
-git-union-merge.1
-git-recover-repository
-git-recover-repository.1
-doc/.ikiwiki
-html
-*.tix
-.hpc
-dist
-# Sandboxed builds
-cabal-dev
-# Project-local emacs configuration
-.dir-locals.el
-# OSX related
-.DS_Store
-.virthualenv
diff --git a/Annex.hs b/Annex.hs
index ae56ec5ad..583cb0e02 100644
--- a/Annex.hs
+++ b/Annex.hs
@@ -5,14 +5,13 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE GeneralizedNewtypeDeriving #-}
+{-# LANGUAGE GeneralizedNewtypeDeriving, PackageImports #-}
 
 module Annex (
 	Annex,
 	AnnexState(..),
 	PreferredContentMap,
 	new,
-	newState,
 	run,
 	eval,
 	getState,
@@ -41,6 +40,7 @@ import Control.Concurrent
 import Common
 import qualified Git
 import qualified Git.Config
+import Annex.Direct.Fixup
 import Git.CatFile
 import Git.CheckAttr
 import Git.CheckIgnore
@@ -111,10 +111,10 @@ data AnnexState = AnnexState
 	, useragent :: Maybe String
 	}
 
-newState :: Git.Repo -> AnnexState
-newState gitrepo = AnnexState
-	{ repo = gitrepo
-	, gitconfig = extractGitConfig gitrepo
+newState :: GitConfig -> Git.Repo -> AnnexState
+newState c r = AnnexState
+	{ repo = r
+	, gitconfig = c
 	, backends = []
 	, remotes = []
 	, output = defaultMessageState
@@ -148,7 +148,10 @@ newState gitrepo = AnnexState
 {- Makes an Annex state object for the specified git repo.
  - Ensures the config is read, if it was not already. -}
 new :: Git.Repo -> IO AnnexState
-new = newState <$$> Git.Config.read
+new r = do
+	r' <- Git.Config.read r
+	let c = extractGitConfig r'
+	newState c <$> if annexDirect c then fixupDirect r' else return r'
 
 {- Performs an action in the Annex monad from a starting state,
  - returning a new state. -}
diff --git a/Annex/Branch.hs b/Annex/Branch.hs
index 8192804a6..9838af25f 100644
--- a/Annex/Branch.hs
+++ b/Annex/Branch.hs
@@ -29,6 +29,7 @@ module Annex.Branch (
 import qualified Data.ByteString.Lazy.Char8 as L
 import qualified Data.Set as S
 import qualified Data.Map as M
+import qualified Control.Exception as E
 
 import Common.Annex
 import Annex.BranchState
@@ -53,6 +54,7 @@ import Logs.Trust.Pure
 import Annex.ReplaceFile
 import qualified Annex.Queue
 import Annex.Branch.Transitions
+import Annex.Exception
 
 {- Name of the branch that is used to store git-annex's information. -}
 name :: Git.Ref
@@ -345,15 +347,15 @@ withIndex' bootstrapping a = do
 #endif
 	let g' = g { gitEnv = Just $ ("GIT_INDEX_FILE", f):e }
 
-	Annex.changeState $ \s -> s { Annex.repo = g' }
-	checkIndexOnce $ unlessM (liftIO $ doesFileExist f) $ do
-		unless bootstrapping create
-		liftIO $ createDirectoryIfMissing True $ takeDirectory f
-		unless bootstrapping $ inRepo genIndex
-	r <- a
+	r <- tryAnnex $ do
+		Annex.changeState $ \s -> s { Annex.repo = g' }
+		checkIndexOnce $ unlessM (liftIO $ doesFileExist f) $ do
+			unless bootstrapping create
+			createAnnexDirectory $ takeDirectory f
+			unless bootstrapping $ inRepo genIndex
+		a
 	Annex.changeState $ \s -> s { Annex.repo = (Annex.repo s) { gitEnv = gitEnv g} }
-
-	return r
+	either E.throw return r
 
 {- Updates the branch's index to reflect the current contents of the branch.
  - Any changes staged in the index will be preserved.
@@ -384,7 +386,7 @@ setIndexSha :: Git.Ref -> Annex ()
 setIndexSha ref = do
 	f <- fromRepo gitAnnexIndexStatus
 	liftIO $ writeFile f $ show ref ++ "\n"
-	setAnnexPerm f
+	setAnnexFilePerm f
 
 {- Stages the journal into the index and returns an action that will
  - clean up the staged journal files, which should only be run once
diff --git a/Annex/CatFile.hs b/Annex/CatFile.hs
index 407b4ddae..812d032c6 100644
--- a/Annex/CatFile.hs
+++ b/Annex/CatFile.hs
@@ -27,6 +27,7 @@ import qualified Annex
 import Git.Types
 import Git.FilePath
 import Git.FileMode
+import qualified Git.Ref
 
 catFile :: Git.Branch -> FilePath -> Annex L.ByteString
 catFile branch file = do
@@ -109,9 +110,6 @@ catKeyChecked needhead ref@(Ref r) =
 
 {- From a file in the repository back to the key.
  -
- - Prefixing the file with ./ makes this work even if in a subdirectory
- - of a repo.
- -
  - Ideally, this should reflect the key that's staged in the index,
  - not the key that's committed to HEAD. Unfortunately, git cat-file
  - does not refresh the index file after it's started up, so things
@@ -134,8 +132,8 @@ catKeyChecked needhead ref@(Ref r) =
 catKeyFile :: FilePath -> Annex (Maybe Key)
 catKeyFile f = ifM (Annex.getState Annex.daemon)
 	( catKeyFileHEAD f
-	, catKeyChecked True (Ref $ ":./" ++ f)
+	, catKeyChecked True $ Git.Ref.fileRef f
 	)
 
 catKeyFileHEAD :: FilePath -> Annex (Maybe Key)
-catKeyFileHEAD f = catKeyChecked False (Ref $ "HEAD:./" ++ f)
+catKeyFileHEAD f = catKeyChecked False $ Git.Ref.fileFromRef Git.Ref.headRef f
diff --git a/Annex/Content.hs b/Annex/Content.hs
index 66ca7be18..62f1b1ccb 100644
--- a/Annex/Content.hs
+++ b/Annex/Content.hs
@@ -29,8 +29,8 @@ module Annex.Content (
 	preseedTmp,
 	freezeContent,
 	thawContent,
-	cleanObjectLoc,
 	dirKeys,
+	withObjectLoc,
 ) where
 
 import System.IO.Unsafe (unsafeInterleaveIO)
@@ -54,9 +54,7 @@ import Annex.Perms
 import Annex.Link
 import Annex.Content.Direct
 import Annex.ReplaceFile
-#ifndef mingw32_HOST_OS
 import Annex.Exception
-#endif
 
 {- Checks if a given key's content is currently present. -}
 inAnnex :: Key -> Annex Bool
@@ -255,11 +253,9 @@ moveAnnex key src = withObjectLoc key storeobject storedirect
   where
 	storeobject dest = ifM (liftIO $ doesFileExist dest)
 		( alreadyhave
-		, do
-			createContentDir dest
+		, modifyContent dest $ do
 			liftIO $ moveFile src dest
 			freezeContent dest
-			freezeContentDir dest
 		)
 	storeindirect = storeobject =<< calcRepo (gitAnnexLocation key)
 
@@ -273,7 +269,6 @@ moveAnnex key src = withObjectLoc key storeobject storedirect
 	storedirect = storedirect' storeindirect
 	storedirect' fallback [] = fallback
 	storedirect' fallback (f:fs) = do
-		thawContentDir =<< calcRepo (gitAnnexLocation key)
 		thawContent src
 		v <- isAnnexLink f
 		if Just key == v
@@ -349,11 +344,11 @@ withObjectLoc key indirect direct = ifM isDirect
   where
 	goindirect = indirect =<< calcRepo (gitAnnexLocation key)
 
-cleanObjectLoc :: Key -> Annex ()
-cleanObjectLoc key = do
+cleanObjectLoc :: Key -> Annex () -> Annex ()
+cleanObjectLoc key cleaner = do
 	file <- calcRepo $ gitAnnexLocation key
-	unlessM crippledFileSystem $
-		void $ liftIO $ catchMaybeIO $ allowWrite $ parentDir file
+	void $ tryAnnexIO $ thawContentDir file
+	cleaner
 	liftIO $ removeparents file (3 :: Int)
   where
 	removeparents _ 0 = noop
@@ -369,13 +364,10 @@ cleanObjectLoc key = do
 removeAnnex :: Key -> Annex ()
 removeAnnex key = withObjectLoc key remove removedirect
   where
-	remove file = do
-		thawContentDir file
+	remove file = cleanObjectLoc key $ do
 		liftIO $ nukeFile file
 		removeInodeCache key
-		cleanObjectLoc key
 	removedirect fs = do
-		thawContentDir =<< calcRepo (gitAnnexLocation key)
 		cache <- recordedInodeCache key
 		removeInodeCache key
 		mapM_ (resetfile cache) fs
@@ -389,12 +381,10 @@ removeAnnex key = withObjectLoc key remove removedirect
 
 {- Moves a key's file out of .git/annex/objects/ -}
 fromAnnex :: Key -> FilePath -> Annex ()
-fromAnnex key dest = do
+fromAnnex key dest = cleanObjectLoc key $ do
 	file <- calcRepo $ gitAnnexLocation key
-	thawContentDir file
 	thawContent file
 	liftIO $ moveFile file dest
-	cleanObjectLoc key
 
 {- Moves a key out of .git/annex/objects/ into .git/annex/bad, and
  - returns the file it was moved to. -}
@@ -404,9 +394,8 @@ moveBad key = do
 	bad <- fromRepo gitAnnexBadDir
 	let dest = bad </> takeFileName src
 	createAnnexDirectory (parentDir dest)
-	thawContentDir src
-	liftIO $ moveFile src dest
-	cleanObjectLoc key
+	cleanObjectLoc key $
+		liftIO $ moveFile src dest
 	logStatus key InfoMissing
 	return dest
 
diff --git a/Annex/Content/Direct.hs b/Annex/Content/Direct.hs
index b0b8621e9..a5d71288b 100644
--- a/Annex/Content/Direct.hs
+++ b/Annex/Content/Direct.hs
@@ -10,6 +10,7 @@ module Annex.Content.Direct (
 	associatedFilesRelative,
 	removeAssociatedFile,
 	removeAssociatedFileUnchecked,
+	removeAssociatedFiles,
 	addAssociatedFile,
 	goodContent,
 	recordedInodeCache,
@@ -64,8 +65,8 @@ changeAssociatedFiles key transform = do
 	files <- associatedFilesRelative key
 	let files' = transform files
 	when (files /= files') $ do
-		createContentDir mapping
-		liftIO $ viaTmp write mapping $ unlines files'
+		modifyContent mapping $
+			liftIO $ viaTmp write mapping $ unlines files'
 	top <- fromRepo Git.repoPath
 	return $ map (top </>) files'
   where
@@ -75,6 +76,13 @@ changeAssociatedFiles key transform = do
  		hPutStr h content
 		hClose h
 
+{- Removes the list of associated files. -}
+removeAssociatedFiles :: Key -> Annex ()
+removeAssociatedFiles key = do
+	mapping <- calcRepo $ gitAnnexMapping key
+	modifyContent mapping $
+		liftIO $ nukeFile mapping
+
 {- Removes an associated file. Returns new associatedFiles value.
  - Checks if this was the last copy of the object, and updates location
  - log. -}
@@ -142,16 +150,16 @@ addInodeCache key cache = do
 
 {- Writes inode cache for a key. -}
 writeInodeCache :: Key -> [InodeCache] -> Annex ()
-writeInodeCache key caches = withInodeCacheFile key $ \f -> do
-	createContentDir f
-	liftIO $ writeFile f $
-		unlines $ map showInodeCache caches
+writeInodeCache key caches = withInodeCacheFile key $ \f -> 
+	modifyContent f $
+		liftIO $ writeFile f $
+			unlines $ map showInodeCache caches
 
 {- Removes an inode cache. -}
 removeInodeCache :: Key -> Annex ()
-removeInodeCache key = withInodeCacheFile key $ \f -> do
-	createContentDir f -- also thaws directory
-	liftIO $ nukeFile f
+removeInodeCache key = withInodeCacheFile key $ \f ->
+	modifyContent f $
+		liftIO $ nukeFile f
 
 withInodeCacheFile :: Key -> (FilePath -> Annex a) -> Annex a
 withInodeCacheFile key a = a =<< calcRepo (gitAnnexInodeCache key)
diff --git a/Annex/Direct.hs b/Annex/Direct.hs
index ea2b577b9..3fa5f9362 100644
--- a/Annex/Direct.hs
+++ b/Annex/Direct.hs
@@ -8,13 +8,18 @@
 module Annex.Direct where
 
 import Common.Annex
+import qualified Annex
 import qualified Git
 import qualified Git.LsFiles
 import qualified Git.Merge
 import qualified Git.DiffTree as DiffTree
+import qualified Git.Config
+import qualified Git.Ref
+import qualified Git.Branch
 import Git.Sha
 import Git.FilePath
 import Git.Types
+import Config
 import Annex.CatFile
 import qualified Annex.Queue
 import Logs.Location
@@ -133,28 +138,33 @@ mergeDirect d branch g = do
  - and the commit sha passed in, along with the old sha of the tree
  - before the merge. Uses git diff-tree to find files that changed between
  - the two shas, and applies those changes to the work tree.
+ -
+ - There are really only two types of changes: An old item can be deleted,
+ - or a new item added. Two passes are made, first deleting and then
+ - adding. This is to handle cases where eg, a file is deleted and a
+ - directory is added. The diff-tree output may list these in the opposite
+ - order, but we cannot really add the directory until the file with the
+ - same name is remvoed.
  -}
 mergeDirectCleanup :: FilePath -> Git.Ref -> Git.Ref -> Annex ()
 mergeDirectCleanup d oldsha newsha = do
 	(items, cleanup) <- inRepo $ DiffTree.diffTreeRecursive oldsha newsha
 	makeabs <- flip fromTopFilePath <$> gitRepo
-	forM_ items (updated makeabs)
+	let fsitems = zip (map (makeabs . DiffTree.file) items) items
+	forM_ fsitems $
+		go DiffTree.srcsha DiffTree.srcmode moveout moveout_raw
+	forM_ fsitems $
+		go DiffTree.dstsha DiffTree.dstmode movein movein_raw
 	void $ liftIO cleanup
 	liftIO $ removeDirectoryRecursive d
   where
-	updated makeabs item = do
-		let f = makeabs (DiffTree.file item)
-		void $ tryAnnex $
-			go f DiffTree.srcsha DiffTree.srcmode moveout moveout_raw
-		void $ tryAnnex $ 
-			go f DiffTree.dstsha DiffTree.dstmode movein movein_raw
-	  where
-		go f getsha getmode a araw
-			| getsha item == nullSha = noop
-			| otherwise = maybe (araw f) (\k -> void $ a k f)
-					=<< catKey (getsha item) (getmode item)
-
-	moveout = removeDirect
+	go getsha getmode a araw (f, item)
+		| getsha item == nullSha = noop
+		| otherwise = void $
+			tryAnnex . maybe (araw f) (\k -> void $ a k f)
+				=<< catKey (getsha item) (getmode item)
+
+	moveout k f = removeDirect k f
 
 	{- Files deleted by the merge are removed from the work tree.
 	 - Empty work tree directories are removed, per git behavior. -}
@@ -200,11 +210,11 @@ toDirectGen k f = do
   where
   	fromindirect loc = do
 		{- Move content from annex to direct file. -}
-		thawContentDir loc
 		updateInodeCache k loc
 		void $ addAssociatedFile k f
-		thawContent loc
-		replaceFile f $ liftIO . moveFile loc
+		modifyContent loc $ do
+			thawContent loc
+			replaceFile f $ liftIO . moveFile loc
 	fromdirect loc = do
 		replaceFile f $
 			liftIO . void . copyFileExternal loc
@@ -231,3 +241,66 @@ changedDirect oldk f = do
 	locs <- removeAssociatedFile oldk f
 	whenM (pure (null locs) <&&> not <$> inAnnex oldk) $
 		logStatus oldk InfoMissing
+
+{- Enable/disable direct mode. -}
+setDirect :: Bool -> Annex ()
+setDirect wantdirect = do
+	if wantdirect
+		then do
+			switchHEAD
+			setbare
+		else do
+			setbare
+			switchHEADBack
+	setConfig (annexConfig "direct") val
+	Annex.changeGitConfig $ \c -> c { annexDirect = wantdirect }
+  where
+	val = Git.Config.boolConfig wantdirect
+	setbare = setConfig (ConfigKey Git.Config.coreBare) val
+
+{- Since direct mode sets core.bare=true, incoming pushes could change
+ - the currently checked out branch. To avoid this problem, HEAD
+ - is changed to a internal ref that nothing is going to push to.
+ -
+ - For refs/heads/master, use refs/heads/annex/direct/master;
+ - this way things that show HEAD (eg shell prompts) will
+ - hopefully show just "master". -}
+directBranch :: Ref -> Ref
+directBranch orighead = case split "/" $ show orighead of
+	("refs":"heads":"annex":"direct":_) -> orighead
+	("refs":"heads":rest) ->
+		Ref $ "refs/heads/annex/direct/" ++ intercalate "/" rest
+	_ -> Ref $ "refs/heads/" ++ show (Git.Ref.base orighead)
+
+{- Converts a directBranch back to the original branch.
+ -
+ - Any other ref is left unchanged.
+ -}
+fromDirectBranch :: Ref -> Ref
+fromDirectBranch directhead = case split "/" $ show directhead of
+	("refs":"heads":"annex":"direct":rest) -> 
+		Ref $ "refs/heads/" ++ intercalate "/" rest
+	_ -> directhead
+
+switchHEAD :: Annex ()
+switchHEAD = maybe noop switch =<< inRepo Git.Branch.currentUnsafe
+  where
+	switch orighead = do
+		let newhead = directBranch orighead
+		maybe noop (inRepo . Git.Branch.update newhead)
+			=<< inRepo (Git.Ref.sha orighead)
+		inRepo $ Git.Branch.checkout newhead
+
+switchHEADBack :: Annex ()
+switchHEADBack = maybe noop switch =<< inRepo Git.Branch.currentUnsafe
+  where
+	switch currhead = do
+		let orighead = fromDirectBranch currhead
+		v <- inRepo $ Git.Ref.sha currhead
+		case v of
+			Just headsha
+				| orighead /= currhead -> do
+					inRepo $ Git.Branch.update orighead headsha
+					inRepo $ Git.Branch.checkout orighead
+					inRepo $ Git.Branch.delete currhead
+			_ -> inRepo $ Git.Branch.checkout orighead
diff --git a/Annex/Direct/Fixup.hs b/Annex/Direct/Fixup.hs
new file mode 100644
index 000000000..13485242a
--- /dev/null
+++ b/Annex/Direct/Fixup.hs
@@ -0,0 +1,31 @@
+{- git-annex direct mode guard fixup
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Annex.Direct.Fixup where
+
+import Git.Types
+import Git.Config
+import qualified Git.Construct as Construct
+import Utility.Path
+import Utility.SafeCommand
+
+{- Direct mode repos have core.bare=true, but are not really bare.
+ - Fix up the Repo to be a non-bare repo, and arrange for git commands
+ - run by git-annex to be passed parameters that override this setting. -}
+fixupDirect :: Repo -> IO Repo
+fixupDirect r@(Repo { location = l@(Local { gitdir = d, worktree = Nothing }) }) = do
+	let r' = r
+		{ location = l { worktree = Just (parentDir d) }
+		, gitGlobalOpts = gitGlobalOpts r ++
+			[ Param "-c"
+			, Param $ coreBare ++ "=" ++ boolConfig False
+			]
+		}
+	-- Recalc now that the worktree is correct.
+	rs' <- Construct.fromRemotes r'
+	return $ r' { remotes = rs' }
+fixupDirect r = return r
diff --git a/Annex/Exception.hs b/Annex/Exception.hs
index aaa6811a5..91347583e 100644
--- a/Annex/Exception.hs
+++ b/Annex/Exception.hs
@@ -10,6 +10,8 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE PackageImports #-}
+
 module Annex.Exception (
 	bracketIO,
 	tryAnnex,
diff --git a/Annex/Hook.hs b/Annex/Hook.hs
new file mode 100644
index 000000000..7301a0958
--- /dev/null
+++ b/Annex/Hook.hs
@@ -0,0 +1,42 @@
+{- git-annex git hooks
+ -
+ - Note that it's important that the scripts not change, otherwise
+ - removing old hooks using an old version of the script would fail.
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Annex.Hook where
+
+import Common.Annex
+import qualified Git.Hook as Git
+import Utility.Shell
+import Config
+
+preCommitHook :: Git.Hook
+preCommitHook = Git.Hook "pre-commit" (mkHookScript "git annex pre-commit .")
+
+mkHookScript :: String -> String
+mkHookScript s = unlines
+	[ shebang_local
+	, "# automatically configured by git-annex"
+	, s
+	]
+
+hookWrite :: Git.Hook -> Annex ()
+hookWrite h = 
+	-- cannot have git hooks in a crippled filesystem (no execute bit)
+	unlessM crippledFileSystem $
+		unlessM (inRepo $ Git.hookWrite h) $
+			hookWarning h "already exists, not configuring"
+
+hookUnWrite :: Git.Hook -> Annex ()
+hookUnWrite h = unlessM (inRepo $ Git.hookUnWrite h) $
+	hookWarning h "contents modified; not deleting. Edit it to remove call to git annex."
+
+hookWarning :: Git.Hook -> String -> Annex ()
+hookWarning h msg = do
+	r <- gitRepo
+	warning $ Git.hookName h ++ " hook (" ++ Git.hookFile h r ++ ") " ++ msg
diff --git a/Annex/Path.hs b/Annex/Path.hs
new file mode 100644
index 000000000..a8c4907b2
--- /dev/null
+++ b/Annex/Path.hs
@@ -0,0 +1,34 @@
+{- git-annex program path
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# LANGUAGE CPP #-}
+
+module Annex.Path where
+
+import Common
+import Config.Files
+import System.Environment
+
+{- A fully qualified path to the currently running git-annex program.
+ - 
+ - getExecutablePath is available since ghc 7.4.2. On OSs it supports
+ - well, it returns the complete path to the program. But, on other OSs,
+ - it might return just the basename.
+ -}
+programPath :: IO (Maybe FilePath)
+programPath = do
+#if MIN_VERSION_base(4,6,0)
+	exe <- getExecutablePath
+	p <- if isAbsolute exe
+		then return exe
+		else readProgramFile
+#else
+	p <- readProgramFile
+#endif
+	-- In case readProgramFile returned just the command name,
+	-- fall back to finding it in PATH.
+	searchPath p
diff --git a/Annex/Perms.hs b/Annex/Perms.hs
index f5925b741..e3a2fa65a 100644
--- a/Annex/Perms.hs
+++ b/Annex/Perms.hs
@@ -6,19 +6,22 @@
  -}
 
 module Annex.Perms (
-	setAnnexPerm,
+	setAnnexFilePerm,
+	setAnnexDirPerm,
 	annexFileMode,
 	createAnnexDirectory,
 	noUmask,
 	createContentDir,
 	freezeContentDir,
 	thawContentDir,
+	modifyContent,
 ) where
 
 import Common.Annex
 import Utility.FileMode
 import Git.SharedRepository
 import qualified Annex
+import Annex.Exception
 import Config
 
 import System.Posix.Types
@@ -31,17 +34,27 @@ withShared a = maybe startup a =<< Annex.getState Annex.shared
 		Annex.changeState $ \s -> s { Annex.shared = Just shared }
 		a shared
 
+setAnnexFilePerm :: FilePath -> Annex ()
+setAnnexFilePerm = setAnnexPerm False
+
+setAnnexDirPerm :: FilePath -> Annex ()
+setAnnexDirPerm = setAnnexPerm True
+
 {- Sets appropriate file mode for a file or directory in the annex,
  - other than the content files and content directory. Normally,
  - use the default mode, but with core.sharedRepository set,
  - allow the group to write, etc. -}
-setAnnexPerm :: FilePath -> Annex ()
-setAnnexPerm file = unlessM crippledFileSystem $
+setAnnexPerm :: Bool -> FilePath -> Annex ()
+setAnnexPerm isdir file = unlessM crippledFileSystem $
 	withShared $ liftIO . go
   where
-	go GroupShared = groupWriteRead file
+	go GroupShared = modifyFileMode file $ addModes $
+		groupSharedModes ++
+		if isdir then [ ownerExecuteMode, groupExecuteMode ] else []
 	go AllShared = modifyFileMode file $ addModes $
-		[ ownerWriteMode, groupWriteMode ] ++ readModes
+		readModes ++
+		[ ownerWriteMode, groupWriteMode ] ++
+		if isdir then executeModes else []
 	go _ = noop
 
 {- Gets the appropriate mode to use for creating a file in the annex
@@ -52,10 +65,7 @@ annexFileMode = withShared $ return . go
 	go GroupShared = sharedmode
 	go AllShared = combineModes (sharedmode:readModes)
 	go _ = stdFileMode
-	sharedmode = combineModes
-		[ ownerWriteMode, groupWriteMode
-		, ownerReadMode, groupReadMode
-		]
+	sharedmode = combineModes groupSharedModes
 
 {- Creates a directory inside the gitAnnexDir, including any parent
  - directories. Makes directories with appropriate permissions. -}
@@ -72,7 +82,7 @@ createAnnexDirectory dir = traverse dir [] =<< top
 	  where
 		done = forM_ below $ \p -> do
 			liftIO $ createDirectoryIfMissing True p
-			setAnnexPerm p
+			setAnnexDirPerm p
 
 {- Blocks writing to the directory an annexed file is in, to prevent the
  - file accidentially being deleted. However, if core.sharedRepository
@@ -103,3 +113,13 @@ createContentDir dest = do
 		liftIO $ allowWrite dir
   where
 	dir = parentDir dest
+
+{- Creates the content directory for a file if it doesn't already exist,
+ - or thaws it if it does, then runs an action to modify the file, and
+ - finally, freezes the content directory. -}
+modifyContent :: FilePath -> Annex a -> Annex a
+modifyContent f a = do
+	createContentDir f -- also thaws it
+	v <- tryAnnex a
+	freezeContentDir f
+	either throwAnnex return v
diff --git a/Annex/Version.hs b/Annex/Version.hs
index 05b3f0227..2b4a49fd2 100644
--- a/Annex/Version.hs
+++ b/Annex/Version.hs
@@ -19,18 +19,21 @@ defaultVersion :: Version
 defaultVersion = "3"
 
 directModeVersion :: Version
-directModeVersion = "4"
+directModeVersion = "5"
 
 supportedVersions :: [Version]
 supportedVersions = [defaultVersion, directModeVersion]
 
 upgradableVersions :: [Version]
 #ifndef mingw32_HOST_OS
-upgradableVersions = ["0", "1", "2"]
+upgradableVersions = ["0", "1", "2", "4"]
 #else
-upgradableVersions = ["2"]
+upgradableVersions = ["2", "4"]
 #endif
 
+autoUpgradeableVersions :: [Version]
+autoUpgradeableVersions = ["4"]
+
 versionField :: ConfigKey
 versionField = annexConfig "version"
 
@@ -42,12 +45,3 @@ setVersion = setConfig versionField
 
 removeVersion :: Annex ()
 removeVersion = unsetConfig versionField
-
-checkVersion :: Version -> Annex ()
-checkVersion v
-	| v `elem` supportedVersions = noop
-	| v `elem` upgradableVersions = err "Upgrade this repository: git-annex upgrade"
-	| otherwise = err "Upgrade git-annex."
-  where
-	err msg = error $ "Repository version " ++ v ++
-		" is not supported. " ++ msg
diff --git a/Assistant.hs b/Assistant.hs
index 781089e06..d4786f99a 100644
--- a/Assistant.hs
+++ b/Assistant.hs
@@ -28,6 +28,8 @@ import Assistant.Threads.ProblemFixer
 import Assistant.Threads.MountWatcher
 #endif
 import Assistant.Threads.NetWatcher
+import Assistant.Threads.Upgrader
+import Assistant.Threads.UpgradeWatcher
 import Assistant.Threads.TransferScanner
 import Assistant.Threads.TransferPoller
 import Assistant.Threads.ConfigMonitor
@@ -50,6 +52,7 @@ import qualified Utility.Daemon
 import Utility.LogFile
 import Utility.ThreadScheduler
 import Utility.HumanTime
+import Annex.Perms
 import qualified Build.SysConfig as SysConfig
 
 import System.Log.Logger
@@ -63,11 +66,13 @@ stopDaemon = liftIO . Utility.Daemon.stopDaemon =<< fromRepo gitAnnexPidFile
  -
  - startbrowser is passed the url and html shim file, as well as the original
  - stdout and stderr descriptors. -}
-startDaemon :: Bool -> Bool -> Maybe Duration -> Maybe HostName ->  Maybe (Maybe Handle -> Maybe Handle -> String -> FilePath -> IO ()) -> Annex ()
-startDaemon assistant foreground startdelay listenhost startbrowser = do
+startDaemon :: Bool -> Bool -> Maybe Duration -> Maybe String -> Maybe HostName ->  Maybe (Maybe Handle -> Maybe Handle -> String -> FilePath -> IO ()) -> Annex ()
+startDaemon assistant foreground startdelay cannotrun listenhost startbrowser = do
 	Annex.changeState $ \s -> s { Annex.daemon = True }
 	pidfile <- fromRepo gitAnnexPidFile
 	logfile <- fromRepo gitAnnexLogFile
+#ifndef mingw32_HOST_OS
+	createAnnexDirectory (parentDir logfile)
 	logfd <- liftIO $ openLog logfile
 	if foreground
 		then do
@@ -86,6 +91,13 @@ startDaemon assistant foreground startdelay listenhost startbrowser = do
 					Just a -> Just $ a origout origerr
 		else
 			start (Utility.Daemon.daemonize logfd (Just pidfile) False) Nothing
+#else
+	-- Windows is always foreground, and has no log file.
+	start id $
+		case startbrowser of
+			Nothing -> Nothing
+			Just a -> Just $ a Nothing Nothing
+#endif
   where
   	desc
 		| assistant = "assistant"
@@ -99,7 +111,6 @@ startDaemon assistant foreground startdelay listenhost startbrowser = do
 			flip runAssistant (go webappwaiter) 
 				=<< newAssistantData st dstatus
 
-
 #ifdef WITH_WEBAPP
 	go webappwaiter = do
 		d <- getAssistant id
@@ -108,44 +119,53 @@ startDaemon assistant foreground startdelay listenhost startbrowser = do
 #endif
 		notice ["starting", desc, "version", SysConfig.packageversion]
 		urlrenderer <- liftIO newUrlRenderer
-		mapM_ (startthread urlrenderer)
-			[ watch $ commitThread
 #ifdef WITH_WEBAPP
-			, assist $ webAppThread d urlrenderer False listenhost Nothing webappwaiter
+		let webappthread = [ assist $ webAppThread d urlrenderer False cannotrun listenhost Nothing webappwaiter ]
+#else
+		let webappthread = []
+#endif
+		let threads = if isJust cannotrun
+			then webappthread
+			else webappthread ++
+				[ watch $ commitThread
+#ifdef WITH_WEBAPP
 #ifdef WITH_PAIRING
-			, assist $ pairListenerThread urlrenderer
+				, assist $ pairListenerThread urlrenderer
 #endif
 #ifdef WITH_XMPP
-			, assist $ xmppClientThread urlrenderer
-			, assist $ xmppSendPackThread urlrenderer
-			, assist $ xmppReceivePackThread urlrenderer
+				, assist $ xmppClientThread urlrenderer
+				, assist $ xmppSendPackThread urlrenderer
+				, assist $ xmppReceivePackThread urlrenderer
 #endif
 #endif
-			, assist $ pushThread
-			, assist $ pushRetryThread
-			, assist $ mergeThread
-			, assist $ transferWatcherThread
-			, assist $ transferPollerThread
-			, assist $ transfererThread
-			, assist $ daemonStatusThread
-			, assist $ sanityCheckerDailyThread
-			, assist $ sanityCheckerHourlyThread
-			, assist $ problemFixerThread urlrenderer
+				, assist $ pushThread
+				, assist $ pushRetryThread
+				, assist $ mergeThread
+				, assist $ transferWatcherThread
+				, assist $ transferPollerThread
+				, assist $ transfererThread
+				, assist $ daemonStatusThread
+				, assist $ sanityCheckerDailyThread
+				, assist $ sanityCheckerHourlyThread
+				, assist $ problemFixerThread urlrenderer
 #ifdef WITH_CLIBS
-			, assist $ mountWatcherThread urlrenderer
+				, assist $ mountWatcherThread urlrenderer
 #endif
-			, assist $ netWatcherThread
-			, assist $ netWatcherFallbackThread
-			, assist $ transferScannerThread urlrenderer
-			, assist $ cronnerThread urlrenderer
-			, assist $ configMonitorThread
-			, assist $ glacierThread
-			, watch $ watchThread
-			-- must come last so that all threads that wait
-			-- on it have already started waiting
-			, watch $ sanityCheckerStartupThread startdelay
-			]
+				, assist $ netWatcherThread
+				, assist $ upgraderThread urlrenderer
+				, assist $ upgradeWatcherThread urlrenderer
+				, assist $ netWatcherFallbackThread
+				, assist $ transferScannerThread urlrenderer
+				, assist $ cronnerThread urlrenderer
+				, assist $ configMonitorThread
+				, assist $ glacierThread
+				, watch $ watchThread
+				-- must come last so that all threads that wait
+				-- on it have already started waiting
+				, watch $ sanityCheckerStartupThread startdelay
+				]
 	
+		mapM_ (startthread urlrenderer) threads
 		liftIO waitForTermination
 
 	watch a = (True, a)
diff --git a/Assistant/Alert.hs b/Assistant/Alert.hs
index b10a724ed..c767d429d 100644
--- a/Assistant/Alert.hs
+++ b/Assistant/Alert.hs
@@ -15,6 +15,7 @@ import Assistant.Alert.Utility
 import qualified Remote
 import Utility.Tense
 import Logs.Transfer
+import Types.Distribution
 
 import Data.String
 import qualified Data.Text as T
@@ -42,6 +43,7 @@ mkAlertButton autoclose label urlrenderer route = do
 		{ buttonLabel = label
 		, buttonUrl = url
 		, buttonAction = if autoclose then Just close else Nothing
+		, buttonPrimary = True
 		}
 #endif
 
@@ -61,7 +63,7 @@ baseActivityAlert = Alert
 	, alertIcon = Just ActivityIcon
 	, alertCombiner = Nothing
 	, alertName = Nothing
-	, alertButton = Nothing
+	, alertButtons = []
 	}
 
 warningAlert :: String -> String -> Alert
@@ -77,11 +79,11 @@ warningAlert name msg = Alert
 	, alertIcon = Just ErrorIcon
 	, alertCombiner = Just $ dataCombiner $ \_old new -> new
 	, alertName = Just $ WarningAlert name
-	, alertButton = Nothing
+	, alertButtons = []
 	}
 
-errorAlert :: String -> AlertButton -> Alert
-errorAlert msg button = Alert
+errorAlert :: String -> [AlertButton] -> Alert
+errorAlert msg buttons = Alert
 	{ alertClass = Error
 	, alertHeader = Nothing
 	, alertMessageRender = renderData
@@ -93,7 +95,7 @@ errorAlert msg button = Alert
 	, alertIcon = Just ErrorIcon
 	, alertCombiner = Nothing
 	, alertName = Nothing
-	, alertButton = Just button
+	, alertButtons = buttons
 	}
 
 activityAlert :: Maybe TenseText -> [TenseChunk] -> Alert
@@ -160,7 +162,7 @@ sanityCheckFixAlert msg = Alert
 	, alertIcon = Just ErrorIcon
 	, alertName = Just SanityCheckFixAlert
 	, alertCombiner = Just $ dataCombiner (++)
-	, alertButton = Nothing
+	, alertButtons = []
 	}
   where
 	render alert = tenseWords $ alerthead : alertData alert ++ [alertfoot]
@@ -172,7 +174,7 @@ fsckingAlert button mr = baseActivityAlert
 	{ alertData = case mr of
 		Nothing -> [ UnTensed $ T.pack $ "Consistency check in progress" ]
 		Just r -> [ UnTensed $ T.pack $ "Consistency check of " ++ Remote.name r ++ " in progress"]
-	, alertButton = Just button
+	, alertButtons = [button]
 	}
 
 showFscking :: UrlRenderer -> Maybe Remote -> IO (Either E.SomeException a) -> Assistant a
@@ -192,7 +194,7 @@ notFsckedNudge urlrenderer mr = do
 	button <- mkAlertButton True (T.pack "Configure") urlrenderer ConfigFsckR
 	void $ addAlert (notFsckedAlert mr button)
 #else
-notFsckedNudge _ = noop
+notFsckedNudge _ _ = noop
 #endif
 
 notFsckedAlert :: Maybe Remote -> AlertButton -> Alert
@@ -204,7 +206,7 @@ notFsckedAlert mr button = Alert
 		]
 	, alertIcon = Just InfoIcon
 	, alertPriority = High
-	, alertButton = Just button
+	, alertButtons = [button]
 	, alertClosable = True
 	, alertClass = Message
 	, alertMessageRender = renderData
@@ -215,7 +217,50 @@ notFsckedAlert mr button = Alert
 	, alertData = []
 	}
 
-brokenRepositoryAlert :: AlertButton -> Alert
+baseUpgradeAlert :: [AlertButton] -> TenseText -> Alert
+baseUpgradeAlert buttons message = Alert
+	{ alertHeader = Just message
+	, alertIcon = Just UpgradeIcon
+	, alertPriority = High
+	, alertButtons = buttons
+	, alertClosable = True
+	, alertClass = Message
+	, alertMessageRender = renderData
+	, alertCounter = 0
+	, alertBlockDisplay = True
+	, alertName = Just UpgradeAlert
+	, alertCombiner = Just $ fullCombiner $ \new _old -> new
+	, alertData = []
+	}
+
+canUpgradeAlert :: AlertPriority -> GitAnnexVersion -> AlertButton -> Alert
+canUpgradeAlert priority version button = 
+	(baseUpgradeAlert [button] $ fromString msg)
+		{ alertPriority = priority
+		, alertData = [fromString $ " (version " ++ version ++ ")"]
+		}
+  where
+	msg = if priority >= High
+		then "An important upgrade of git-annex is available!"
+		else "An upgrade of git-annex is available."
+
+upgradeReadyAlert :: AlertButton -> Alert
+upgradeReadyAlert button = baseUpgradeAlert [button] $
+	fromString "A new version of git-annex has been installed."
+
+upgradingAlert :: Alert
+upgradingAlert = activityAlert Nothing [ fromString "Upgrading git-annex" ]
+
+upgradeFinishedAlert :: Maybe AlertButton -> GitAnnexVersion -> Alert
+upgradeFinishedAlert button version =
+	baseUpgradeAlert (maybe [] (:[]) button) $ fromString $ 
+		"Finished upgrading git-annex to version " ++ version
+
+upgradeFailedAlert :: String -> Alert
+upgradeFailedAlert msg = (errorAlert msg [])
+	{ alertHeader = Just $ fromString "Upgrade failed." }
+
+brokenRepositoryAlert :: [AlertButton] -> Alert
 brokenRepositoryAlert = errorAlert "Serious problems have been detected with your repository. This needs your immediate attention!"
 
 repairingAlert :: String -> Alert
@@ -228,7 +273,7 @@ pairingAlert :: AlertButton -> Alert
 pairingAlert button = baseActivityAlert
 	{ alertData = [ UnTensed "Pairing in progress" ]
 	, alertPriority = High
-	, alertButton = Just button
+	, alertButtons = [button]
 	}
 
 pairRequestReceivedAlert :: String -> AlertButton -> Alert
@@ -244,7 +289,7 @@ pairRequestReceivedAlert who button = Alert
 	, alertIcon = Just InfoIcon
 	, alertName = Just $ PairAlert who
 	, alertCombiner = Just $ dataCombiner $ \_old new -> new
-	, alertButton = Just button
+	, alertButtons = [button]
 	}
 
 pairRequestAcknowledgedAlert :: String -> Maybe AlertButton -> Alert
@@ -253,7 +298,7 @@ pairRequestAcknowledgedAlert who button = baseActivityAlert
 	, alertPriority = High
 	, alertName = Just $ PairAlert who
 	, alertCombiner = Just $ dataCombiner $ \_old new -> new
-	, alertButton = button
+	, alertButtons = maybe [] (:[]) button
 	}
 
 xmppNeededAlert :: AlertButton -> Alert
@@ -261,7 +306,7 @@ xmppNeededAlert button = Alert
 	{ alertHeader = Just "Share with friends, and keep your devices in sync across the cloud."
 	, alertIcon = Just TheCloud
 	, alertPriority = High
-	, alertButton = Just button
+	, alertButtons = [button]
 	, alertClosable = True
 	, alertClass = Message
 	, alertMessageRender = renderData
@@ -280,7 +325,7 @@ cloudRepoNeededAlert friendname button = Alert
 		]
 	, alertIcon = Just ErrorIcon
 	, alertPriority = High
-	, alertButton = Just button
+	, alertButtons = [button]
 	, alertClosable = True
 	, alertClass = Message
 	, alertMessageRender = renderData
@@ -298,7 +343,7 @@ remoteRemovalAlert desc button = Alert
 		"\" has been emptied, and can now be removed."
 	, alertIcon = Just InfoIcon
 	, alertPriority = High
-	, alertButton = Just button
+	, alertButtons = [button]
 	, alertClosable = True
 	, alertClass = Message
 	, alertMessageRender = renderData
diff --git a/Assistant/Alert/Utility.hs b/Assistant/Alert/Utility.hs
index af52a4235..db2ea1925 100644
--- a/Assistant/Alert/Utility.hs
+++ b/Assistant/Alert/Utility.hs
@@ -87,7 +87,7 @@ makeAlertFiller success alert
 		{ alertClass = if c == Activity then c' else c
 		, alertPriority = Filler
 		, alertClosable = True
-		, alertButton = Nothing
+		, alertButtons = []
 		, alertIcon = Just $ if success then SuccessIcon else ErrorIcon
 		}
   where
diff --git a/Assistant/MakeRemote.hs b/Assistant/MakeRemote.hs
index 32a3fd6f5..bf316e49d 100644
--- a/Assistant/MakeRemote.hs
+++ b/Assistant/MakeRemote.hs
@@ -20,6 +20,7 @@ import qualified Command.InitRemote
 import Logs.UUID
 import Logs.Remote
 import Git.Remote
+import Git.Types (RemoteName)
 import Creds
 import Assistant.Gpg
 import Utility.Gpg (KeyId)
diff --git a/Assistant/NamedThread.hs b/Assistant/NamedThread.hs
index 2440c45bf..e1b3983f7 100644
--- a/Assistant/NamedThread.hs
+++ b/Assistant/NamedThread.hs
@@ -82,7 +82,7 @@ startNamedThread urlrenderer (NamedThread afterstartupsanitycheck name a) = do
 					(RestartThreadR name)
 				runAssistant d $ void $ addAlert $
 					(warningAlert (fromThreadName name) msg)
-						{ alertButton = Just button }
+						{ alertButtons = [button] }
 #endif
 
 namedThreadId :: NamedThread -> Assistant (Maybe ThreadId)
diff --git a/Assistant/Pairing.hs b/Assistant/Pairing.hs
index 4736c4396..bb1384a15 100644
--- a/Assistant/Pairing.hs
+++ b/Assistant/Pairing.hs
@@ -28,7 +28,7 @@ data PairStage
 	| PairAck
 	{- "I saw your PairAck; you can stop sending them." -}
 	| PairDone
-	deriving (Eq, Read, Show, Ord)
+	deriving (Eq, Read, Show, Ord, Enum)
 
 newtype PairMsg = PairMsg (Verifiable (PairStage, PairData, SomeAddr))
 	deriving (Eq, Read, Show)
diff --git a/Assistant/Ssh.hs b/Assistant/Ssh.hs
index f316aa500..1dc982ba6 100644
--- a/Assistant/Ssh.hs
+++ b/Assistant/Ssh.hs
@@ -12,6 +12,7 @@ import Utility.Tmp
 import Utility.UserInfo
 import Utility.Shell
 import Utility.Rsync
+import Utility.FileMode
 import Git.Remote
 
 import Data.Text (Text)
@@ -233,12 +234,8 @@ setupSshKeyPair sshkeypair sshdata = do
 	sshdir <- sshDir
 	createDirectoryIfMissing True $ parentDir $ sshdir </> sshprivkeyfile
 
-	unlessM (doesFileExist $ sshdir </> sshprivkeyfile) $ do
-		h <- fdToHandle =<<
-			createFile (sshdir </> sshprivkeyfile)
-				(unionFileModes ownerWriteMode ownerReadMode)
-		hPutStr h (sshPrivKey sshkeypair)
-		hClose h
+	unlessM (doesFileExist $ sshdir </> sshprivkeyfile) $
+		writeFileProtected (sshdir </> sshprivkeyfile) (sshPrivKey sshkeypair)
 	unlessM (doesFileExist $ sshdir </> sshpubkeyfile) $
 		writeFile (sshdir </> sshpubkeyfile) (sshPubKey sshkeypair)
 
diff --git a/Assistant/Threads/NetWatcher.hs b/Assistant/Threads/NetWatcher.hs
index 0d8442c69..a7124fa01 100644
--- a/Assistant/Threads/NetWatcher.hs
+++ b/Assistant/Threads/NetWatcher.hs
@@ -15,6 +15,7 @@ import Assistant.Sync
 import Utility.ThreadScheduler
 import qualified Types.Remote as Remote
 import Assistant.DaemonStatus
+import Utility.NotificationBroadcaster
 
 #if WITH_DBUS
 import Utility.DBus
@@ -127,7 +128,9 @@ listenWicdConnections client callback =
 #endif
 
 handleConnection :: Assistant ()
-handleConnection = reconnectRemotes True =<< networkRemotes
+handleConnection = do
+	liftIO . sendNotification . networkConnectedNotifier =<< getDaemonStatus
+	reconnectRemotes True =<< networkRemotes
 
 {- Network remotes to sync with. -}
 networkRemotes :: Assistant [Remote]
diff --git a/Assistant/Threads/PairListener.hs b/Assistant/Threads/PairListener.hs
index 482b0923c..cd95ab5a4 100644
--- a/Assistant/Threads/PairListener.hs
+++ b/Assistant/Threads/PairListener.hs
@@ -16,6 +16,7 @@ import Assistant.WebApp.Types
 import Assistant.Alert
 import Assistant.DaemonStatus
 import Utility.ThreadScheduler
+import Utility.Format
 import Git
 
 import Network.Multicast
@@ -42,20 +43,32 @@ pairListenerThread urlrenderer = namedThread "PairListener" $ do
 			(pip, verified) <- verificationCheck m
 				=<< (pairingInProgress <$> getDaemonStatus)
 			let wrongstage = maybe False (\p -> pairMsgStage m <= inProgressPairStage p) pip
-			case (wrongstage, sane, pairMsgStage m) of
-				-- ignore our own messages, and
-				-- out of order messages
-				(True, _, _) -> go reqs cache sock
-				(_, False, _) -> go reqs cache sock
-				(_, _, PairReq) -> if m `elem` reqs
+			let fromus = maybe False (\p -> remoteSshPubKey (pairMsgData m) == remoteSshPubKey (inProgressPairData p)) pip
+			case (wrongstage, fromus, sane, pairMsgStage m) of
+				(_, True, _, _) -> do
+					debug ["ignoring message that looped back"]
+					go reqs cache sock
+				(_, _, False, _) -> go reqs cache sock
+				-- PairReq starts a pairing process, so a
+				-- new one is always heeded, even if
+				-- some other pairing is in process.
+				(_, _, _, PairReq) -> if m `elem` reqs
 					then go reqs (invalidateCache m cache) sock
 					else do
 						pairReqReceived verified urlrenderer m
 						go (m:take 10 reqs) (invalidateCache m cache) sock
-				(_, _, PairAck) -> do
+				(True, _, _, _) -> do
+					debug
+						["ignoring out of order message"
+						, show (pairMsgStage m)
+						, "expected"
+						, show (succ . inProgressPairStage <$> pip)
+						]
+					go reqs cache sock
+				(_, _, _, PairAck) -> do
 					cache' <- pairAckReceived verified pip m cache
 					go reqs cache' sock
-				(_, _, PairDone) -> do
+				(_,_ , _, PairDone) -> do
 					pairDoneReceived verified pip m
 					go reqs cache sock
 
@@ -75,11 +88,10 @@ pairListenerThread urlrenderer = namedThread "PairListener" $ do
 		verified = verifiedPairMsg m pip
 		sameuuid = pairUUID (inProgressPairData pip) == pairUUID (pairMsgData m)
 		
-	{- Various sanity checks on the content of the message. -}
-	checkSane msg 
+	checkSane msg
 		{- Control characters could be used in a
 		 - console poisoning attack. -}
-		| any isControl msg || any (`elem` "\r\n") msg = do
+		| any isControl (filter (/= '\n') (decode_c msg)) = do
 			liftAnnex $ warning
 				"illegal control characters in pairing message; ignoring"
 			return False
diff --git a/Assistant/Threads/SanityChecker.hs b/Assistant/Threads/SanityChecker.hs
index b03298510..6946e8b3a 100644
--- a/Assistant/Threads/SanityChecker.hs
+++ b/Assistant/Threads/SanityChecker.hs
@@ -25,8 +25,10 @@ import Utility.Batch
 import Utility.NotificationBroadcaster
 import Config
 import Utility.HumanTime
+import Git.Repair
 
 import Data.Time.Clock.POSIX
+import qualified Data.Set as S
 
 {- This thread runs once at startup, and most other threads wait for it
  - to finish. (However, the webapp thread does not, to prevent the UI
@@ -36,6 +38,21 @@ sanityCheckerStartupThread startupdelay = namedThreadUnchecked "SanityCheckerSta
 	{- Stale git locks can prevent commits from happening, etc. -}
 	void $ repairStaleGitLocks =<< liftAnnex gitRepo
 
+	{- A corrupt index file can prevent the assistant from working at
+	 - all, so detect and repair. -}
+	ifM (not <$> liftAnnex (inRepo (checkIndex S.empty)))
+		( do
+			notice ["corrupt index file found at startup; removing and restaging"]
+			liftAnnex $ inRepo nukeIndex
+			{- Normally the startup scan avoids re-staging files,
+			 - but with the index deleted, everything needs to be
+			 - restaged. -}
+			modifyDaemonStatus_ $ \s -> s { forceRestage = True }
+		, whenM (liftAnnex $ inRepo missingIndex) $ do
+			debug ["no index file; restaging"]
+			modifyDaemonStatus_ $ \s -> s { forceRestage = True }
+		)
+
 	{- If there's a startup delay, it's done here. -}
 	liftIO $ maybe noop (threadDelaySeconds . Seconds . fromIntegral . durationSeconds) startupdelay
 
diff --git a/Assistant/Threads/TransferWatcher.hs b/Assistant/Threads/TransferWatcher.hs
index fc09373e7..cd7282865 100644
--- a/Assistant/Threads/TransferWatcher.hs
+++ b/Assistant/Threads/TransferWatcher.hs
@@ -16,6 +16,7 @@ import Utility.DirWatcher.Types
 import qualified Remote
 
 import Control.Concurrent
+import qualified Data.Map as M
 
 {- This thread watches for changes to the gitAnnexTransferDir,
  - and updates the DaemonStatus's map of ongoing transfers. -}
@@ -89,6 +90,11 @@ onDel file = case parseTransferFile file of
 		debug [ "transfer finishing:", show t]
 		minfo <- removeTransfer t
 
+		-- Run transfer hook.
+		m <- transferHook <$> getDaemonStatus
+		maybe noop (\hook -> void $ liftIO $ forkIO $ hook t)
+			(M.lookup (transferKey t) m)
+
 		finished <- asIO2 finishedTransfer
 		void $ liftIO $ forkIO $ do
 			{- XXX race workaround delay. The location
diff --git a/Assistant/Threads/UpgradeWatcher.hs b/Assistant/Threads/UpgradeWatcher.hs
new file mode 100644
index 000000000..80f2040a0
--- /dev/null
+++ b/Assistant/Threads/UpgradeWatcher.hs
@@ -0,0 +1,109 @@
+{- git-annex assistant thread to detect when git-annex is upgraded
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# LANGUAGE CPP #-}
+
+module Assistant.Threads.UpgradeWatcher (
+	upgradeWatcherThread
+) where
+
+import Assistant.Common
+import Assistant.Upgrade
+import Utility.DirWatcher
+import Utility.DirWatcher.Types
+import Utility.ThreadScheduler
+import Assistant.Types.UrlRenderer
+import Assistant.Alert
+import Assistant.DaemonStatus
+#ifdef WITH_WEBAPP
+import Assistant.WebApp.Types
+import qualified Build.SysConfig
+#endif
+
+import Control.Concurrent.MVar
+import qualified Data.Text as T
+
+data WatcherState = InStartupScan | Started | Upgrading
+	deriving (Eq)
+
+upgradeWatcherThread :: UrlRenderer -> NamedThread
+upgradeWatcherThread urlrenderer = namedThread "UpgradeWatcher" $ do
+	whenM (liftIO checkSuccessfulUpgrade) $
+		showSuccessfulUpgrade urlrenderer
+	go =<< liftIO upgradeFlagFile
+  where
+	go Nothing = debug [ "cannot determine program path" ]
+	go (Just flagfile) = do
+		mvar <- liftIO $ newMVar InStartupScan
+		changed <- Just <$> asIO2 (changedFile urlrenderer mvar flagfile)
+		let hooks = mkWatchHooks
+			{ addHook = changed
+			, delHook = changed
+			, addSymlinkHook = changed
+			, modifyHook = changed
+			, delDirHook = changed
+			}
+		let dir = parentDir flagfile
+		let depth = length (splitPath dir) + 1
+		let nosubdirs f = length (splitPath f) == depth
+		void $ liftIO $ watchDir dir nosubdirs hooks (startup mvar)
+  	-- Ignore bogus events generated during the startup scan.
+  	startup mvar scanner = do
+		r <- scanner
+		void $ swapMVar mvar Started
+		return r
+
+changedFile :: UrlRenderer -> MVar WatcherState -> FilePath -> FilePath -> Maybe FileStatus -> Assistant ()
+changedFile urlrenderer mvar flagfile file _status
+	| flagfile /= file = noop
+	| otherwise = do
+		state <- liftIO $ readMVar mvar
+		when (state == Started) $ do
+			setstate Upgrading
+			ifM (liftIO upgradeSanityCheck)
+				( handleUpgrade urlrenderer
+				, do
+					debug ["new version failed sanity check; not using"]
+					setstate Started
+				)
+  where
+	setstate = void . liftIO . swapMVar mvar
+
+handleUpgrade :: UrlRenderer -> Assistant ()
+handleUpgrade urlrenderer = do
+	-- Wait 2 minutes for any final upgrade changes to settle.
+	-- (For example, other associated files may be being put into
+	-- place.) Not needed when using a distribution bundle, because
+	-- in that case git-annex handles the upgrade in a non-racy way.
+	liftIO $ unlessM usingDistribution $
+		threadDelaySeconds (Seconds 120)
+	ifM autoUpgradeEnabled
+		( do
+			debug ["starting automatic upgrade"]
+			unattendedUpgrade
+#ifdef WITH_WEBAPP
+		, do
+			button <- mkAlertButton True (T.pack "Finish Upgrade") urlrenderer ConfigFinishUpgradeR
+			void $ addAlert $ upgradeReadyAlert button
+#else
+		, noop
+#endif
+		)
+
+showSuccessfulUpgrade :: UrlRenderer -> Assistant ()
+showSuccessfulUpgrade urlrenderer = do
+#ifdef WITH_WEBAPP
+	button <- ifM autoUpgradeEnabled 
+		( pure Nothing
+		, Just <$> mkAlertButton True
+			(T.pack "Enable Automatic Upgrades")
+			urlrenderer ConfigEnableAutomaticUpgradeR
+		)
+	void $ addAlert $ upgradeFinishedAlert button Build.SysConfig.packageversion
+#else
+	noop
+#endif
diff --git a/Assistant/Threads/Upgrader.hs b/Assistant/Threads/Upgrader.hs
new file mode 100644
index 000000000..f0c47e844
--- /dev/null
+++ b/Assistant/Threads/Upgrader.hs
@@ -0,0 +1,101 @@
+{- git-annex assistant thread to detect when upgrade is available
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# LANGUAGE CPP #-}
+
+module Assistant.Threads.Upgrader (
+	upgraderThread
+) where
+
+import Assistant.Common
+import Assistant.Upgrade
+
+import Assistant.Types.UrlRenderer
+import Assistant.DaemonStatus
+import Assistant.Alert
+import Utility.NotificationBroadcaster
+import Utility.Tmp
+import qualified Annex
+import qualified Build.SysConfig
+import qualified Utility.Url as Url
+import qualified Annex.Url as Url
+import qualified Git.Version
+import Types.Distribution
+#ifdef WITH_WEBAPP
+import Assistant.WebApp.Types
+#endif
+
+import Data.Time.Clock
+import qualified Data.Text as T
+
+upgraderThread :: UrlRenderer -> NamedThread
+upgraderThread urlrenderer = namedThread "Upgrader" $
+	when (isJust Build.SysConfig.upgradelocation) $ do
+		{- Check for upgrade on startup, unless it was just
+		 - upgraded. -}
+		unlessM (liftIO checkSuccessfulUpgrade) $
+			checkUpgrade urlrenderer
+		h <- liftIO . newNotificationHandle False . networkConnectedNotifier =<< getDaemonStatus
+		go h =<< liftIO getCurrentTime
+  where
+  	{- Wait for a network connection event. Then see if it's been
+	 - half a day since the last upgrade check. If so, proceed with
+	 - check. -}
+	go h lastchecked = do
+		liftIO $ waitNotification h
+		autoupgrade <- liftAnnex $ annexAutoUpgrade <$> Annex.getGitConfig
+		if autoupgrade == NoAutoUpgrade
+			then go h lastchecked
+			else do
+				now <- liftIO getCurrentTime
+				if diffUTCTime now lastchecked > halfday
+					then do
+						checkUpgrade urlrenderer
+						go h =<< liftIO getCurrentTime
+					else go h lastchecked
+	halfday = 12 * 60 * 60
+
+checkUpgrade :: UrlRenderer -> Assistant ()
+checkUpgrade urlrenderer = do
+	debug [ "Checking if an upgrade is available." ]
+	go =<< getDistributionInfo
+  where
+	go Nothing = debug [ "Failed to check if upgrade is available." ]
+	go (Just d) = do
+		let installed = Git.Version.normalize Build.SysConfig.packageversion
+		let avail = Git.Version.normalize $ distributionVersion d
+		let old = Git.Version.normalize <$> distributionUrgentUpgrade d
+		if Just installed <= old
+			then canUpgrade High urlrenderer d
+			else if installed < avail
+				then canUpgrade Low urlrenderer d
+				else debug [ "No new version found." ]
+
+canUpgrade :: AlertPriority -> UrlRenderer -> GitAnnexDistribution -> Assistant ()
+canUpgrade urgency urlrenderer d = ifM autoUpgradeEnabled
+	( startDistributionDownload d
+	, do
+#ifdef WITH_WEBAPP
+		button <- mkAlertButton True (T.pack "Upgrade") urlrenderer (ConfigStartUpgradeR d)
+		void $ addAlert (canUpgradeAlert urgency (distributionVersion d) button)
+#else
+		noop
+#endif
+	)
+
+getDistributionInfo :: Assistant (Maybe GitAnnexDistribution)
+getDistributionInfo = do
+	ua <- liftAnnex Url.getUserAgent
+	liftIO $ withTmpFile "git-annex.tmp" $ \tmpfile h -> do
+		hClose h
+		ifM (Url.downloadQuiet distributionInfoUrl [] [] tmpfile ua)
+			( readish <$> readFileStrict tmpfile
+			, return Nothing
+			)
+
+distributionInfoUrl :: String
+distributionInfoUrl = fromJust Build.SysConfig.upgradelocation ++ ".info"
diff --git a/Assistant/Threads/Watcher.hs b/Assistant/Threads/Watcher.hs
index 3eedbe145..6a56eadbb 100644
--- a/Assistant/Threads/Watcher.hs
+++ b/Assistant/Threads/Watcher.hs
@@ -200,6 +200,9 @@ onAdd matcher file filestatus
 			add matcher file
 	| otherwise = noChange
 
+shouldRestage :: DaemonStatus -> Bool
+shouldRestage ds = scanComplete ds || forceRestage ds
+
 {- In direct mode, add events are received for both new files, and
  - modified existing files.
  -}
@@ -214,7 +217,7 @@ onAddDirect symlinkssupported matcher file fs = do
 				 - really modified, but it might have
 				 - just been deleted and been put back,
 				 - so it symlink is restaged to make sure. -}
-				( ifM (scanComplete <$> getDaemonStatus)
+				( ifM (shouldRestage <$> getDaemonStatus)
 					( do
 						link <- liftAnnex $ inRepo $ gitAnnexLink file key
 						addLink file link (Just key)
@@ -286,7 +289,7 @@ onAddSymlink' linktarget mk isdirect file filestatus = go mk
 	 - links too.)
 	 -}
 	ensurestaged (Just link) daemonstatus
-		| scanComplete daemonstatus = addLink file link mk
+		| shouldRestage daemonstatus = addLink file link mk
 		| otherwise = case filestatus of
 			Just s
 				| not (afterLastDaemonRun (statusChangeTime s) daemonstatus) -> noChange
diff --git a/Assistant/Threads/WebApp.hs b/Assistant/Threads/WebApp.hs
index a5f4f4201..2ad61168e 100644
--- a/Assistant/Threads/WebApp.hs
+++ b/Assistant/Threads/WebApp.hs
@@ -30,6 +30,7 @@ import Assistant.WebApp.Configurators.Preferences
 import Assistant.WebApp.Configurators.Edit
 import Assistant.WebApp.Configurators.Delete
 import Assistant.WebApp.Configurators.Fsck
+import Assistant.WebApp.Configurators.Upgrade
 import Assistant.WebApp.Documentation
 import Assistant.WebApp.Control
 import Assistant.WebApp.OtherRepos
@@ -52,11 +53,12 @@ webAppThread
 	:: AssistantData
 	-> UrlRenderer
 	-> Bool
+	-> Maybe String
 	-> Maybe HostName
 	-> Maybe (IO Url)
 	-> Maybe (Url -> FilePath -> IO ())
 	-> NamedThread
-webAppThread assistantdata urlrenderer noannex listenhost postfirstrun onstartup = thread $ liftIO $ do
+webAppThread assistantdata urlrenderer noannex cannotrun listenhost postfirstrun onstartup = thread $ liftIO $ do
 #ifdef __ANDROID__
 	when (isJust listenhost) $
 		-- See Utility.WebApp
@@ -68,6 +70,7 @@ webAppThread assistantdata urlrenderer noannex listenhost postfirstrun onstartup
 		<*> getreldir
 		<*> pure staticRoutes
 		<*> pure postfirstrun
+		<*> pure cannotrun
 		<*> pure noannex
 		<*> pure listenhost
 	setUrlRenderer urlrenderer $ yesodRender webapp (pack "")
diff --git a/Assistant/TransferSlots.hs b/Assistant/TransferSlots.hs
index 36d557c3d..cb66e845a 100644
--- a/Assistant/TransferSlots.hs
+++ b/Assistant/TransferSlots.hs
@@ -5,6 +5,8 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE CPP #-}
+
 module Assistant.TransferSlots where
 
 import Assistant.Common
@@ -32,8 +34,10 @@ import qualified Data.Map as M
 import qualified Control.Exception as E
 import Control.Concurrent
 import qualified Control.Concurrent.MSemN as MSemN
-import System.Posix.Signals (signalProcessGroup, sigTERM, sigKILL)
+#ifndef mingw32_HOST_OS
 import System.Posix.Process (getProcessGroupIDOf)
+import System.Posix.Signals (signalProcessGroup, sigTERM, sigKILL)
+#endif
 
 type TransferGenerator = Assistant (Maybe (Transfer, TransferInfo, Transferrer -> Assistant ()))
 
@@ -247,13 +251,18 @@ cancelTransfer pause t = do
 	signalthread tid
 		| pause = throwTo tid PauseTransfer
 		| otherwise = killThread tid
-	{- In order to stop helper processes like rsync,
-	 - kill the whole process group of the process running the transfer. -}
 	killproc pid = void $ tryIO $ do
+#ifndef mingw32_HOST_OS
+		{- In order to stop helper processes like rsync,
+		 - kill the whole process group of the process
+		 - running the transfer. -}
 		g <- getProcessGroupIDOf pid
 		void $ tryIO $ signalProcessGroup sigTERM g
 		threadDelay 50000 -- 0.05 second grace period
 		void $ tryIO $ signalProcessGroup sigKILL g
+#else
+		error "TODO: cancelTransfer not implemented on Windows"
+#endif
 
 {- Start or resume a transfer. -}
 startTransfer :: Transfer -> Assistant ()
diff --git a/Assistant/TransferrerPool.hs b/Assistant/TransferrerPool.hs
index d9104f74d..bb4648731 100644
--- a/Assistant/TransferrerPool.hs
+++ b/Assistant/TransferrerPool.hs
@@ -5,12 +5,17 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE CPP #-}
+
 module Assistant.TransferrerPool where
 
 import Assistant.Common
 import Assistant.Types.TransferrerPool
 import Logs.Transfer
+
+#ifndef mingw32_HOST_OS
 import qualified Command.TransferKeys as T
+#endif
 
 import Control.Concurrent.STM
 import System.Process (create_group)
@@ -38,13 +43,18 @@ withTransferrer program pool a = do
  - finish. -}
 performTransfer :: Transferrer -> Transfer -> AssociatedFile -> IO Bool
 performTransfer transferrer t f = catchBoolIO $ do
+#ifndef mingw32_HOST_OS
 	T.sendRequest t f (transferrerWrite transferrer)
 	T.readResponse (transferrerRead transferrer)
+#else
+	error "TODO performTransfer not implemented on Windows"
+#endif
 
 {- Starts a new git-annex transferkeys process, setting up a pipe
  - that will be used to communicate with it. -}
 mkTransferrer :: FilePath -> IO Transferrer
 mkTransferrer program = do
+#ifndef mingw32_HOST_OS
 	(myread, twrite) <- createPipe
 	(tread, mywrite) <- createPipe
 	mapM_ (\fd -> setFdOption fd CloseOnExec True) [myread, mywrite]
@@ -68,6 +78,9 @@ mkTransferrer program = do
 		, transferrerWrite = mywriteh
 		, transferrerHandle = pid
 		}
+#else
+	error "TODO mkTransferrer not implemented on Windows"
+#endif
 
 {- Checks if a Transferrer is still running. If not, makes a new one. -}
 checkTransferrer :: FilePath -> Transferrer -> IO Transferrer
diff --git a/Assistant/Types/Alert.hs b/Assistant/Types/Alert.hs
index 2e52ca7ef..e6fbe86d3 100644
--- a/Assistant/Types/Alert.hs
+++ b/Assistant/Types/Alert.hs
@@ -31,6 +31,7 @@ data AlertName
 	| CloudRepoNeededAlert
 	| SyncAlert
 	| NotFsckedAlert
+	| UpgradeAlert
 	deriving (Eq)
 
 {- The first alert is the new alert, the second is an old alert.
@@ -49,10 +50,10 @@ data Alert = Alert
 	, alertIcon :: Maybe AlertIcon
 	, alertCombiner :: Maybe AlertCombiner
 	, alertName :: Maybe AlertName
-	, alertButton :: Maybe AlertButton
+	, alertButtons :: [AlertButton]
 	}
 
-data AlertIcon = ActivityIcon | SyncIcon | SuccessIcon | ErrorIcon | InfoIcon | TheCloud
+data AlertIcon = ActivityIcon | SyncIcon | SuccessIcon | ErrorIcon | InfoIcon | UpgradeIcon | TheCloud
 
 type AlertMap = M.Map AlertId Alert
 
@@ -73,4 +74,5 @@ data AlertButton = AlertButton
 	{ buttonLabel :: Text
 	, buttonUrl :: Text
 	, buttonAction :: Maybe (AlertId -> IO ())
+	, buttonPrimary :: Bool
 	}
diff --git a/Assistant/Types/DaemonStatus.hs b/Assistant/Types/DaemonStatus.hs
index a1a0d64dc..a618c700d 100644
--- a/Assistant/Types/DaemonStatus.hs
+++ b/Assistant/Types/DaemonStatus.hs
@@ -14,6 +14,7 @@ import Logs.Transfer
 import Assistant.Types.ThreadName
 import Assistant.Types.NetMessager
 import Assistant.Types.Alert
+import Utility.Url
 
 import Control.Concurrent.STM
 import Control.Concurrent.MVar
@@ -28,6 +29,8 @@ data DaemonStatus = DaemonStatus
 	{ startedThreads :: M.Map ThreadName (Async (), IO ())
 	-- False when the daemon is performing its startup scan
 	, scanComplete :: Bool
+	-- True when all files should be restaged.
+	, forceRestage :: Bool
 	-- Time when a previous process of the daemon was running ok
 	, lastRunning :: Maybe POSIXTime
 	-- True when the daily sanity checker is running
@@ -53,18 +56,25 @@ data DaemonStatus = DaemonStatus
 	, desynced :: S.Set UUID
 	-- Pairing request that is in progress.
 	, pairingInProgress :: Maybe PairingInProgress
-	-- Broadcasts notifications about all changes to the DaemonStatus
+	-- Broadcasts notifications about all changes to the DaemonStatus.
 	, changeNotifier :: NotificationBroadcaster
 	-- Broadcasts notifications when queued or current transfers change.
 	, transferNotifier :: NotificationBroadcaster
-	-- Broadcasts notifications when there's a change to the alerts
+	-- Broadcasts notifications when there's a change to the alerts.
 	, alertNotifier :: NotificationBroadcaster
-	-- Broadcasts notifications when the syncRemotes change
+	-- Broadcasts notifications when the syncRemotes change.
 	, syncRemotesNotifier :: NotificationBroadcaster
-	-- Broadcasts notifications when the scheduleLog changes
+	-- Broadcasts notifications when the scheduleLog changes.
 	, scheduleLogNotifier :: NotificationBroadcaster
 	-- Broadcasts a notification once the startup sanity check has run.
 	, startupSanityCheckNotifier :: NotificationBroadcaster
+	-- Broadcasts notifications when the network is connected.
+	, networkConnectedNotifier :: NotificationBroadcaster
+	-- Broadcasts notifications when a global redirect is needed.
+	, globalRedirNotifier :: NotificationBroadcaster
+	, globalRedirUrl :: Maybe URLString
+	-- Actions to run after a Key is transferred.
+	, transferHook :: M.Map Key (Transfer -> IO ())
 	-- When the XMPP client is connected, this will contain the XMPP
 	-- address.
 	, xmppClientID :: Maybe ClientID
@@ -81,6 +91,7 @@ newDaemonStatus :: IO DaemonStatus
 newDaemonStatus = DaemonStatus
 	<$> pure M.empty
 	<*> pure False
+	<*> pure False
 	<*> pure Nothing
 	<*> pure False
 	<*> pure Nothing
@@ -100,5 +111,9 @@ newDaemonStatus = DaemonStatus
 	<*> newNotificationBroadcaster
 	<*> newNotificationBroadcaster
 	<*> newNotificationBroadcaster
+	<*> newNotificationBroadcaster
+	<*> newNotificationBroadcaster
+	<*> pure Nothing
+	<*> pure M.empty
 	<*> pure Nothing
 	<*> pure M.empty
diff --git a/Assistant/XMPP.hs b/Assistant/XMPP.hs
index 0360ce860..09b7daf4e 100644
--- a/Assistant/XMPP.hs
+++ b/Assistant/XMPP.hs
@@ -21,7 +21,7 @@ import qualified Data.Map as M
 import Data.ByteString (ByteString)
 import qualified Data.ByteString as B
 import Data.XML.Types
-import qualified Codec.Binary.Base64 as B64
+import qualified "dataenc" Codec.Binary.Base64 as B64
 
 {- Name of the git-annex tag, in our own XML namespace.
  - (Not using a namespace URL to avoid unnecessary bloat.) -}
diff --git a/Build/BundledPrograms.hs b/Build/BundledPrograms.hs
index d071ae3aa..3c53f06fb 100644
--- a/Build/BundledPrograms.hs
+++ b/Build/BundledPrograms.hs
@@ -30,6 +30,7 @@ bundledPrograms = catMaybes
 #endif
 	, Just "rsync"
 	, Just "ssh"
+	, Just "ssh-keygen"
 #ifndef mingw32_HOST_OS
 	, Just "sh"
 #endif
@@ -44,6 +45,11 @@ bundledPrograms = catMaybes
 	, SysConfig.sha512
 	, SysConfig.sha224
 	, SysConfig.sha384
+#ifdef linux_HOST_OS
+	-- used to unpack the tarball when upgrading
+	, Just "gunzip"
+	, Just "tar"
+#endif
 	-- nice and ionice are not included in the bundle; we rely on the
 	-- system's own version, which may better match its kernel
 	]
diff --git a/Build/Configure.hs b/Build/Configure.hs
index 262ac2080..d17f6cbf0 100644
--- a/Build/Configure.hs
+++ b/Build/Configure.hs
@@ -7,7 +7,7 @@ import Data.List
 import System.Process
 import Control.Applicative
 import System.FilePath
-import System.Environment
+import System.Environment (getArgs)
 import Data.Maybe
 import Control.Monad.IfElse
 import Data.Char
@@ -17,11 +17,13 @@ import Build.Version
 import Utility.SafeCommand
 import Utility.Monad
 import Utility.ExternalSHA
+import Utility.Env
 import qualified Git.Version
 
 tests :: [TestCase]
 tests =
 	[ TestCase "version" getVersion
+	, TestCase "UPGRADE_LOCATION" getUpgradeLocation
 	, TestCase "git" $ requireCmd "git" "git --version >/dev/null"
 	, TestCase "git version" getGitVersion
 	, testCp "cp_a" "-a"
@@ -33,6 +35,7 @@ tests =
 	, TestCase "wget" $ testCmd "wget" "wget --version >/dev/null"
 	, TestCase "bup" $ testCmd "bup" "bup --version >/dev/null"
 	, TestCase "quvi" $ testCmd "quvi" "quvi --version >/dev/null"
+	, TestCase "newquvi" $ testCmd "newquvi" "quvi info >/dev/null"
 	, TestCase "nice" $ testCmd "nice" "nice true >/dev/null"
 	, TestCase "ionice" $ testCmd "ionice" "ionice -c3 true >/dev/null"
 	, TestCase "gpg" $ maybeSelectCmd "gpg"
@@ -90,6 +93,11 @@ testCp k option = TestCase cmd $ testCmd k cmdline
 	cmd = "cp " ++ option
 	cmdline = cmd ++ " " ++ testFile ++ " " ++ testFile ++ ".new"
 
+getUpgradeLocation :: Test
+getUpgradeLocation = do
+	e <- getEnv "UPGRADE_LOCATION"
+	return $ Config "upgradelocation" $ MaybeStringConfig e
+
 getGitVersion :: Test
 getGitVersion = Config "gitversion" . StringConfig . show
 	<$> Git.Version.installed
@@ -130,4 +138,3 @@ androidConfig c = overrides ++ filter (not . overridden) c
 		]
 	overridden (Config k _) = k `elem` overridekeys
 	overridekeys = map (\(Config k _) -> k) overrides
-
diff --git a/Build/DistributionUpdate.hs b/Build/DistributionUpdate.hs
new file mode 100644
index 000000000..0afc2211f
--- /dev/null
+++ b/Build/DistributionUpdate.hs
@@ -0,0 +1,64 @@
+{- Builds distributon info files for each git-annex release in a directory
+ - tree, which must itself be part of a git-annex repository. Only files
+ - that are present have their info file created. -}
+
+import Common.Annex
+import Types.Distribution
+import Build.Version
+import Utility.UserInfo
+import Utility.Path
+import qualified Git.Construct
+import qualified Annex
+import Annex.Content
+import Backend
+import Git.Command
+
+import Data.Time.Clock
+
+main = do
+	state <- Annex.new =<< Git.Construct.fromPath =<< getRepoDir
+	Annex.eval state makeinfos
+
+makeinfos :: Annex ()
+makeinfos = do
+	basedir <- liftIO getRepoDir
+	version <- liftIO getChangelogVersion
+	now <- liftIO getCurrentTime
+	liftIO $ putStrLn $ "building info files for version " ++ version ++ " in " ++ basedir
+	fs <- liftIO $ dirContentsRecursiveSkipping (== "info") (basedir </> "git-annex")
+	forM_ fs $ \f -> do
+		v <- lookupFile f
+		case v of
+			Nothing -> noop
+			Just (k, _b) -> whenM (inAnnex k) $ do
+				liftIO $ putStrLn f
+				let infofile = f ++ ".info"
+				liftIO $ writeFile infofile $ show $ GitAnnexDistribution
+					{ distributionUrl = mkUrl basedir f
+					, distributionKey = k
+					, distributionVersion = version
+					, distributionReleasedate = now
+					, distributionUrgentUpgrade = Nothing
+					}
+				void $ inRepo $ runBool [Param "add", Param infofile]
+	void $ inRepo $ runBool 
+		[ Param "commit"
+		, Param "-m"
+		, Param $ "publishing git-annex " ++ version
+		]
+	void $ inRepo $ runBool
+		[ Param "annex"
+		, Params "move --to website"
+		]
+	void $ inRepo $ runBool
+		[ Param "annex"
+		, Params "sync"
+		]
+
+getRepoDir :: IO FilePath
+getRepoDir = do
+	home <- liftIO myHomeDir
+	return $ home </> "lib" </> "downloads"
+
+mkUrl :: FilePath -> FilePath -> String
+mkUrl basedir f = "https://downloads.kitenet.net/" ++ relPathDirToFile basedir f
diff --git a/Build/EvilSplicer.hs b/Build/EvilSplicer.hs
index f40d10033..35dba4968 100644
--- a/Build/EvilSplicer.hs
+++ b/Build/EvilSplicer.hs
@@ -584,7 +584,7 @@ text_builder_hack = replace "Data.Text.Lazy.Builder.Internal.fromText" "Data.Tex
 parsecAndReplace :: Parser String -> String -> String
 parsecAndReplace p s = case parse find "" s of
 	Left e -> s
-	Right l -> concatMap (either (\c -> [c]) id) l
+	Right l -> concatMap (either return id) l
   where
   	find :: Parser [Either Char String]
 	find = many $ try (Right <$> p) <|> (Left <$> anyChar)
diff --git a/Build/OSXMkLibs.hs b/Build/OSXMkLibs.hs
index ed12a945f..dae9bc0ae 100644
--- a/Build/OSXMkLibs.hs
+++ b/Build/OSXMkLibs.hs
@@ -144,7 +144,7 @@ getLibName lib libmap = case M.lookup lib libmap of
 	Just n -> (n, libmap)
 	Nothing -> (nextfreename, M.insert lib nextfreename libmap)
   where
-	names = map (\c -> [c]) ['A' .. 'Z'] ++
+	names = map pure ['A' .. 'Z'] ++
 		[[n, l] | n <- ['0' .. '9'], l <- ['A' .. 'Z']]
 	used = S.fromList $ M.elems libmap
 	nextfreename = fromMaybe (error "ran out of short library names!") $ 
diff --git a/BuildFlags.hs b/BuildFlags.hs
index 40d5bb29b..1dba47eaf 100644
--- a/BuildFlags.hs
+++ b/BuildFlags.hs
@@ -60,4 +60,7 @@ buildFlags = filter (not . null)
 #ifdef WITH_CRYPTOHASH
 	, "CryptoHash"
 #endif
+#ifdef WITH_EKG
+	, "EKG"
+#endif
 	]
diff --git a/Command/Add.hs b/Command/Add.hs
index e0a8269aa..9f1beb28a 100644
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -23,10 +23,11 @@ import Annex.Perms
 import Annex.Link
 import qualified Annex
 import qualified Annex.Queue
+#ifdef WITH_CLIBS
 #ifndef __ANDROID__
 import Utility.Touch
 #endif
-import Utility.FileMode
+#endif
 import Config
 import Utility.InodeCache
 import Annex.FileMatcher
@@ -86,11 +87,6 @@ start file = ifAnnexed file addpresent add
  - So a KeySource is returned. Its inodeCache can be used to detect any
  - changes that might be made to the file after it was locked down.
  -
- - In indirect mode, the write bit is removed from the file as part of lock
- - down to guard against further writes, and because objects in the annex
- - have their write bit disabled anyway. This is not done in direct mode,
- - because files there need to remain writable at all times.
- -
  - When possible, the file is hard linked to a temp directory. This guards
  - against some changes, like deletion or overwrite of the file, and
  - allows lsof checks to be done more efficiently when adding a lot of files.
@@ -103,16 +99,28 @@ lockDown file = ifM crippledFileSystem
 	, do
 		tmp <- fromRepo gitAnnexTmpDir
 		createAnnexDirectory tmp
-		unlessM isDirect $ 
-			void $ liftIO $ tryIO $ preventWrite file
-		liftIO $ catchMaybeIO $ do
+		eitherToMaybe <$> tryAnnexIO (go tmp)
+	)
+  where
+	{- In indirect mode, the write bit is removed from the file as part
+	 - of lock down to guard against further writes, and because objects
+	 - in the annex have their write bit disabled anyway.
+	 -
+	 - Freezing the content early also lets us fail early when
+	 - someone else owns the file.
+	 -
+	 - This is not done in direct mode, because files there need to
+	 - remain writable at all times.
+	-}
+  	go tmp = do
+		unlessM isDirect $
+			freezeContent file
+		liftIO $ do
 			(tmpfile, h) <- openTempFile tmp $
 				relatedTemplate $ takeFileName file
 			hClose h
 			nukeFile tmpfile
 			withhardlink tmpfile `catchIO` const nohardlink
-	)
-  where
   	nohardlink = do
 		cache <- genInodeCache file
 		return KeySource
@@ -205,6 +213,7 @@ link file key mcache = flip catchAnnex (undo file key) $ do
 	l <- inRepo $ gitAnnexLink file key
 	replaceFile file $ makeAnnexLink l
 
+#ifdef WITH_CLIBS
 #ifndef __ANDROID__
 	-- touch symlink to have same time as the original file,
 	-- as provided in the InodeCache
@@ -212,6 +221,7 @@ link file key mcache = flip catchAnnex (undo file key) $ do
 		Just c -> liftIO $ touch file (TimeSpec $ inodeCacheToMtime c) False
 		Nothing -> noop
 #endif
+#endif
 
 	return l
 
diff --git a/Command/Fix.hs b/Command/Fix.hs
index da2627619..a63a10f8f 100644
--- a/Command/Fix.hs
+++ b/Command/Fix.hs
@@ -14,9 +14,11 @@ import System.PosixCompat.Files
 import Common.Annex
 import Command
 import qualified Annex.Queue
+#ifdef WITH_CLIBS
 #ifndef __ANDROID__
 import Utility.Touch
 #endif
+#endif
 
 def :: [Command]
 def = [notDirect $ noCommit $ command "fix" paramPaths seek
@@ -36,17 +38,21 @@ start file (key, _) = do
 perform :: FilePath -> FilePath -> CommandPerform
 perform file link = do
 	liftIO $ do
+#ifdef WITH_CLIBS
 #ifndef __ANDROID__
 		-- preserve mtime of symlink
 		mtime <- catchMaybeIO $ TimeSpec . modificationTime
 			<$> getSymbolicLinkStatus file
 #endif
+#endif
 		createDirectoryIfMissing True (parentDir file)
 		removeFile file
 		createSymbolicLink link file
+#ifdef WITH_CLIBS
 #ifndef __ANDROID__
 		maybe noop (\t -> touch file t False) mtime
 #endif
+#endif
 	next $ cleanup file
 
 cleanup :: FilePath -> CommandCleanup
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
index 3b89c550c..a8e52af98 100644
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -218,9 +218,10 @@ verifyLocationLog key desc = do
 	
 	{- Since we're checking that a key's file is present, throw
 	 - in a permission fixup here too. -}
-	when (present && not direct) $ do
-		file <- calcRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
+	when (present && not direct) $
 		freezeContent file
+	whenM (liftIO $ doesDirectoryExist $ parentDir file) $
 		freezeContentDir file
 
 	{- In direct mode, modified files will show up as not present,
diff --git a/Command/GCryptSetup.hs b/Command/GCryptSetup.hs
index a27e470c1..bdd770f15 100644
--- a/Command/GCryptSetup.hs
+++ b/Command/GCryptSetup.hs
@@ -23,13 +23,17 @@ seek = [withStrings start]
 
 start :: String -> CommandStart
 start gcryptid = next $ next $ do
-	g <- gitRepo
 	u <- getUUID
+	when (u /= NoUUID) $
+		error "gcryptsetup refusing to run; this repository already has a git-annex uuid!"
+	
+	g <- gitRepo
 	gu <- Remote.GCrypt.getGCryptUUID True g
-	if u == NoUUID && gu == Nothing
+	let newgu = genUUIDInNameSpace gCryptNameSpace gcryptid
+	if gu == Nothing || gu == Just newgu
 		then if Git.repoIsLocalBare g
 			then do
 				void $ Remote.GCrypt.setupRepo gcryptid g
 				return True
 			else error "cannot use gcrypt in a non-bare repository"
-		else error "gcryptsetup permission denied"
+		else error "gcryptsetup uuid mismatch"
diff --git a/Command/ImportFeed.hs b/Command/ImportFeed.hs
index 7f54643c9..45a0d3b7e 100644
--- a/Command/ImportFeed.hs
+++ b/Command/ImportFeed.hs
@@ -106,7 +106,7 @@ downloadFeed url = do
 	liftIO $ withTmpFile "feed" $ \f h -> do
 		fileEncoding h
 		ifM (Url.download url [] [] f ua)
-			( liftIO $ parseFeedString <$> hGetContentsStrict h
+			( parseFeedString <$> hGetContentsStrict h
 			, return Nothing
 			)
 
diff --git a/Command/Indirect.hs b/Command/Indirect.hs
index a2512ea96..8b857e2f6 100644
--- a/Command/Indirect.hs
+++ b/Command/Indirect.hs
@@ -20,9 +20,9 @@ import Config
 import qualified Annex
 import Annex.Direct
 import Annex.Content
+import Annex.Content.Direct
 import Annex.CatFile
 import Annex.Version
-import Annex.Perms
 import Annex.Exception
 import Init
 import qualified Command.Add
@@ -77,7 +77,8 @@ perform = do
 			Just s
 				| isSymbolicLink s -> void $ flip whenAnnexed f $
 					\_ (k, _) -> do
-						cleandirect k
+						removeInodeCache k
+						removeAssociatedFiles k
 						return Nothing
 				| otherwise -> 
 					maybe noop (fromdirect f)
@@ -87,8 +88,8 @@ perform = do
 
 	fromdirect f k = do
 		showStart "indirect" f
-		thawContentDir =<< calcRepo (gitAnnexLocation k)
-		cleandirect k -- clean before content directory gets frozen
+		removeInodeCache k
+		removeAssociatedFiles k
 		whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
 			v <-tryAnnexIO (moveAnnex k f)
 			case v of
@@ -103,10 +104,6 @@ perform = do
 	warnlocked e = do
 		warning $ show e
 		warning "leaving this file as-is; correct this problem and run git annex add on it"
-
-	cleandirect k = do
-		liftIO . nukeFile =<< calcRepo (gitAnnexInodeCache k)
-		liftIO . nukeFile =<< calcRepo (gitAnnexMapping k)
 	
 cleanup :: CommandCleanup
 cleanup = do
diff --git a/Command/Info.hs b/Command/Info.hs
new file mode 100644
index 000000000..d465f2d84
--- /dev/null
+++ b/Command/Info.hs
@@ -0,0 +1,384 @@
+{- git-annex command
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# LANGUAGE BangPatterns #-}
+
+module Command.Info where
+
+import "mtl" Control.Monad.State.Strict
+import qualified Data.Map as M
+import Text.JSON
+import Data.Tuple
+import Data.Ord
+import System.PosixCompat.Files
+
+import Common.Annex
+import qualified Remote
+import qualified Command.Unused
+import qualified Git
+import qualified Annex
+import Command
+import Utility.DataUnits
+import Utility.DiskFree
+import Annex.Content
+import Types.Key
+import Logs.UUID
+import Logs.Trust
+import Remote
+import Config
+import Utility.Percentage
+import Logs.Transfer
+import Types.TrustLevel
+import Types.FileMatcher
+import qualified Limit
+
+-- a named computation that produces a statistic
+type Stat = StatState (Maybe (String, StatState String))
+
+-- data about a set of keys
+data KeyData = KeyData
+	{ countKeys :: Integer
+	, sizeKeys :: Integer
+	, unknownSizeKeys :: Integer
+	, backendsKeys :: M.Map String Integer
+	}
+
+data NumCopiesStats = NumCopiesStats
+	{ numCopiesVarianceMap :: M.Map Variance Integer
+	}
+
+newtype Variance = Variance Int
+	deriving (Eq, Ord)
+
+instance Show Variance where
+	show (Variance n)
+		| n >= 0 = "numcopies +" ++ show n
+		| otherwise = "numcopies " ++ show n
+
+-- cached info that multiple Stats use
+data StatInfo = StatInfo
+	{ presentData :: Maybe KeyData
+	, referencedData :: Maybe KeyData
+	, numCopiesStats :: Maybe NumCopiesStats
+	}
+
+-- a state monad for running Stats in
+type StatState = StateT StatInfo Annex
+
+def :: [Command]
+def = [noCommit $ command "info" paramPaths seek
+	SectionQuery "shows general information about the annex"]
+
+seek :: [CommandSeek]
+seek = [withWords start]
+
+start :: [FilePath] -> CommandStart
+start [] = do
+	globalInfo
+	stop
+start ps = do
+	mapM_ localInfo =<< filterM isdir ps
+	stop
+  where
+	isdir = liftIO . catchBoolIO . (isDirectory <$$> getFileStatus)
+
+globalInfo :: Annex ()
+globalInfo = do
+	stats <- selStats global_fast_stats global_slow_stats
+	showCustom "info" $ do
+		evalStateT (mapM_ showStat stats) (StatInfo Nothing Nothing Nothing)
+		return True
+
+localInfo :: FilePath -> Annex ()
+localInfo dir = showCustom (unwords ["info", dir]) $ do
+	stats <- selStats (tostats local_fast_stats) (tostats local_slow_stats)
+	evalStateT (mapM_ showStat stats) =<< getLocalStatInfo dir
+	return True
+  where
+  	tostats = map (\s -> s dir)
+
+selStats :: [Stat] -> [Stat] -> Annex [Stat]
+selStats fast_stats slow_stats = do
+	fast <- Annex.getState Annex.fast
+	return $ if fast
+		then fast_stats
+		else fast_stats ++ slow_stats
+
+{- Order is significant. Less expensive operations, and operations
+ - that share data go together.
+ -}
+global_fast_stats :: [Stat]
+global_fast_stats = 
+	[ repository_mode
+	, remote_list Trusted
+	, remote_list SemiTrusted
+	, remote_list UnTrusted
+	, transfer_list
+	, disk_size
+	]
+global_slow_stats :: [Stat]
+global_slow_stats = 
+	[ tmp_size
+	, bad_data_size
+	, local_annex_keys
+	, local_annex_size
+	, known_annex_files
+	, known_annex_size
+	, bloom_info
+	, backend_usage
+	]
+local_fast_stats :: [FilePath -> Stat]
+local_fast_stats =
+	[ local_dir
+	, const local_annex_keys
+	, const local_annex_size
+	, const known_annex_files
+	, const known_annex_size
+	]
+local_slow_stats :: [FilePath -> Stat]
+local_slow_stats =
+	[ const numcopies_stats
+	]
+
+stat :: String -> (String -> StatState String) -> Stat
+stat desc a = return $ Just (desc, a desc)
+
+nostat :: Stat
+nostat = return Nothing
+
+json :: JSON j => (j -> String) -> StatState j -> String -> StatState String
+json serialize a desc = do
+	j <- a
+	lift $ maybeShowJSON [(desc, j)]
+	return $ serialize j
+
+nojson :: StatState String -> String -> StatState String
+nojson a _ = a
+
+showStat :: Stat -> StatState ()
+showStat s = maybe noop calc =<< s
+  where
+	calc (desc, a) = do
+		(lift . showHeader) desc
+		lift . showRaw =<< a
+
+repository_mode :: Stat
+repository_mode = stat "repository mode" $ json id $ lift $
+	ifM isDirect 
+		( return "direct", return "indirect" )
+
+remote_list :: TrustLevel -> Stat
+remote_list level = stat n $ nojson $ lift $ do
+	us <- M.keys <$> (M.union <$> uuidMap <*> remoteMap Remote.name)
+	rs <- fst <$> trustPartition level us
+	s <- prettyPrintUUIDs n rs
+	return $ if null s then "0" else show (length rs) ++ "\n" ++ beginning s
+  where
+	n = showTrustLevel level ++ " repositories"
+	
+local_dir :: FilePath -> Stat
+local_dir dir = stat "directory" $ json id $ return dir
+
+local_annex_keys :: Stat
+local_annex_keys = stat "local annex keys" $ json show $
+	countKeys <$> cachedPresentData
+
+local_annex_size :: Stat
+local_annex_size = stat "local annex size" $ json id $
+	showSizeKeys <$> cachedPresentData
+
+known_annex_files :: Stat
+known_annex_files = stat "annexed files in working tree" $ json show $
+	countKeys <$> cachedReferencedData
+
+known_annex_size :: Stat
+known_annex_size = stat "size of annexed files in working tree" $ json id $
+	showSizeKeys <$> cachedReferencedData
+
+tmp_size :: Stat
+tmp_size = staleSize "temporary directory size" gitAnnexTmpDir
+
+bad_data_size :: Stat
+bad_data_size = staleSize "bad keys size" gitAnnexBadDir
+
+bloom_info :: Stat
+bloom_info = stat "bloom filter size" $ json id $ do
+	localkeys <- countKeys <$> cachedPresentData
+	capacity <- fromIntegral <$> lift Command.Unused.bloomCapacity
+	let note = aside $
+		if localkeys >= capacity
+		then "appears too small for this repository; adjust annex.bloomcapacity"
+		else showPercentage 1 (percentage capacity localkeys) ++ " full"
+
+	-- Two bloom filters are used at the same time, so double the size
+	-- of one.
+	size <- roughSize memoryUnits False . (* 2) . fromIntegral . fst <$>
+		lift Command.Unused.bloomBitsHashes
+
+	return $ size ++ note
+
+transfer_list :: Stat
+transfer_list = stat "transfers in progress" $ nojson $ lift $ do
+	uuidmap <- Remote.remoteMap id
+	ts <- getTransfers
+	return $ if null ts
+		then "none"
+		else multiLine $
+			map (uncurry $ line uuidmap) $ sort ts
+  where
+	line uuidmap t i = unwords
+		[ showLcDirection (transferDirection t) ++ "ing"
+		, fromMaybe (key2file $ transferKey t) (associatedFile i)
+		, if transferDirection t == Upload then "to" else "from"
+		, maybe (fromUUID $ transferUUID t) Remote.name $
+			M.lookup (transferUUID t) uuidmap
+		]
+
+disk_size :: Stat
+disk_size = stat "available local disk space" $ json id $ lift $
+	calcfree
+		<$> (annexDiskReserve <$> Annex.getGitConfig)
+		<*> inRepo (getDiskFree . gitAnnexDir)
+  where
+	calcfree reserve (Just have) = unwords
+		[ roughSize storageUnits False $ nonneg $ have - reserve
+		, "(+" ++ roughSize storageUnits False reserve
+		, "reserved)"
+		]			
+	calcfree _ _ = "unknown"
+
+	nonneg x
+		| x >= 0 = x
+		| otherwise = 0
+
+backend_usage :: Stat
+backend_usage = stat "backend usage" $ nojson $
+	calc
+		<$> (backendsKeys <$> cachedReferencedData)
+		<*> (backendsKeys <$> cachedPresentData)
+  where
+	calc x y = multiLine $
+		map (\(n, b) -> b ++ ": " ++ show n) $
+		reverse $ sort $ map swap $ M.toList $
+		M.unionWith (+) x y
+
+numcopies_stats :: Stat
+numcopies_stats = stat "numcopies stats" $ nojson $
+	calc <$> (maybe M.empty numCopiesVarianceMap <$> cachedNumCopiesStats)
+  where
+	calc = multiLine
+		. map (\(variance, count) -> show variance ++ ": " ++ show count)
+		. reverse . sortBy (comparing snd) . M.toList
+
+cachedPresentData :: StatState KeyData
+cachedPresentData = do
+	s <- get
+	case presentData s of
+		Just v -> return v
+		Nothing -> do
+			v <- foldKeys <$> lift getKeysPresent
+			put s { presentData = Just v }
+			return v
+
+cachedReferencedData :: StatState KeyData
+cachedReferencedData = do
+	s <- get
+	case referencedData s of
+		Just v -> return v
+		Nothing -> do
+			!v <- lift $ Command.Unused.withKeysReferenced
+				emptyKeyData addKey
+			put s { referencedData = Just v }
+			return v
+
+-- currently only available for local info
+cachedNumCopiesStats :: StatState (Maybe NumCopiesStats)
+cachedNumCopiesStats = numCopiesStats <$> get
+
+getLocalStatInfo :: FilePath -> Annex StatInfo
+getLocalStatInfo dir = do
+	fast <- Annex.getState Annex.fast
+	matcher <- Limit.getMatcher
+	(presentdata, referenceddata, numcopiesstats) <-
+		Command.Unused.withKeysFilesReferencedIn dir initial
+			(update matcher fast)
+	return $ StatInfo (Just presentdata) (Just referenceddata) (Just numcopiesstats)
+  where
+	initial = (emptyKeyData, emptyKeyData, emptyNumCopiesStats)
+	update matcher fast key file vs@(presentdata, referenceddata, numcopiesstats) =
+		ifM (matcher $ FileInfo file file)
+			( do
+				!presentdata' <- ifM (inAnnex key)
+					( return $ addKey key presentdata
+					, return presentdata
+					)
+				let !referenceddata' = addKey key referenceddata
+				!numcopiesstats' <- if fast
+					then return numcopiesstats
+					else updateNumCopiesStats key file numcopiesstats
+				return $! (presentdata', referenceddata', numcopiesstats')
+			, return vs
+			)
+
+emptyKeyData :: KeyData
+emptyKeyData = KeyData 0 0 0 M.empty
+
+emptyNumCopiesStats :: NumCopiesStats
+emptyNumCopiesStats = NumCopiesStats M.empty
+
+foldKeys :: [Key] -> KeyData
+foldKeys = foldl' (flip addKey) emptyKeyData
+
+addKey :: Key -> KeyData -> KeyData
+addKey key (KeyData count size unknownsize backends) =
+	KeyData count' size' unknownsize' backends'
+  where
+	{- All calculations strict to avoid thunks when repeatedly
+	 - applied to many keys. -}
+	!count' = count + 1
+	!backends' = M.insertWith' (+) (keyBackendName key) 1 backends
+	!size' = maybe size (+ size) ks
+	!unknownsize' = maybe (unknownsize + 1) (const unknownsize) ks
+	ks = keySize key
+
+updateNumCopiesStats :: Key -> FilePath -> NumCopiesStats -> Annex NumCopiesStats
+updateNumCopiesStats key file (NumCopiesStats m) = do
+	!variance <- Variance <$> numCopiesCheck file key (-)
+	let !m' = M.insertWith' (+) variance 1 m
+	let !ret = NumCopiesStats m'
+	return ret
+
+showSizeKeys :: KeyData -> String
+showSizeKeys d = total ++ missingnote
+  where
+	total = roughSize storageUnits False $ sizeKeys d
+	missingnote
+		| unknownSizeKeys d == 0 = ""
+		| otherwise = aside $
+			"+ " ++ show (unknownSizeKeys d) ++
+			" unknown size"
+
+staleSize :: String -> (Git.Repo -> FilePath) -> Stat
+staleSize label dirspec = go =<< lift (dirKeys dirspec)
+  where
+	go [] = nostat
+	go keys = onsize =<< sum <$> keysizes keys
+	onsize 0 = nostat
+	onsize size = stat label $
+		json (++ aside "clean up with git-annex unused") $
+			return $ roughSize storageUnits False size
+	keysizes keys = do
+		dir <- lift $ fromRepo dirspec
+		liftIO $ forM keys $ \k -> catchDefaultIO 0 $
+			fromIntegral . fileSize 
+				<$> getFileStatus (dir </> keyFile k)
+
+aside :: String -> String
+aside s = " (" ++ s ++ ")"
+
+multiLine :: [String] -> String
+multiLine = concatMap (\l -> "\n\t" ++ l)
diff --git a/Command/List.hs b/Command/List.hs
index fda8f3dc7..12c27c022 100644
--- a/Command/List.hs
+++ b/Command/List.hs
@@ -22,7 +22,7 @@ import Logs.UUID
 import Annex.UUID
 import qualified Option
 import qualified Annex
-import Git.Remote
+import Git.Types (RemoteName)
 
 def :: [Command]
 def = [noCommit $ withOptions [allrepos] $ command "list" paramPaths seek
diff --git a/Command/Map.hs b/Command/Map.hs
index 41beb4b92..91f4a0251 100644
--- a/Command/Map.hs
+++ b/Command/Map.hs
@@ -74,7 +74,7 @@ drawMap rs umap ts = Dot.graph $ repos ++ trusted ++ others
 
 hostname :: Git.Repo -> String
 hostname r
-	| Git.repoIsUrl r = Git.Url.host r
+	| Git.repoIsUrl r = fromMaybe (Git.repoLocation r) (Git.Url.host r)
 	| otherwise = "localhost"
 
 basehostname :: Git.Repo -> String
diff --git a/Command/Merge.hs b/Command/Merge.hs
index 5d6b2ffd2..31db7a99f 100644
--- a/Command/Merge.hs
+++ b/Command/Merge.hs
@@ -34,6 +34,5 @@ mergeBranch = do
 
 mergeSynced :: CommandStart
 mergeSynced = do
-	branch <- inRepo Git.Branch.current
 	prepMerge
-	maybe stop mergeLocal branch
+	mergeLocal =<< inRepo Git.Branch.current
diff --git a/Command/Reinject.hs b/Command/Reinject.hs
index e4abeef3c..c49af0060 100644
--- a/Command/Reinject.hs
+++ b/Command/Reinject.hs
@@ -14,7 +14,7 @@ import Annex.Content
 import qualified Command.Fsck
 
 def :: [Command]
-def = [notDirect $ command "reinject" (paramPair "SRC" "DEST") seek
+def = [command "reinject" (paramPair "SRC" "DEST") seek
 	SectionUtility "sets content of annexed file"]
 
 seek :: [CommandSeek]
diff --git a/Command/SendKey.hs b/Command/SendKey.hs
index 039a3d7ca..24b1821c3 100644
--- a/Command/SendKey.hs
+++ b/Command/SendKey.hs
@@ -46,6 +46,4 @@ fieldTransfer direction key a = do
 	ok <- maybe (a $ const noop)
 		(\u -> runTransfer (Transfer direction (toUUID u) key) afile noRetry a)
 		=<< Fields.getField Fields.remoteUUID
-	liftIO $ if ok
-		then exitSuccess
-		else exitFailure
+	liftIO $ exitBool ok
diff --git a/Command/Status.hs b/Command/Status.hs
index 44d868f6b..5dc625994 100644
--- a/Command/Status.hs
+++ b/Command/Status.hs
@@ -1,384 +1,89 @@
 {- git-annex command
  -
- - Copyright 2011 Joey Hess <joey@kitenet.net>
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE BangPatterns #-}
-
 module Command.Status where
 
-import "mtl" Control.Monad.State.Strict
-import qualified Data.Map as M
-import Text.JSON
-import Data.Tuple
-import Data.Ord
-import System.PosixCompat.Files
-
 import Common.Annex
-import qualified Remote
-import qualified Command.Unused
-import qualified Git
-import qualified Annex
 import Command
-import Utility.DataUnits
-import Utility.DiskFree
-import Annex.Content
-import Types.Key
-import Logs.UUID
-import Logs.Trust
-import Remote
+import Annex.CatFile
+import Annex.Content.Direct
 import Config
-import Utility.Percentage
-import Logs.Transfer
-import Types.TrustLevel
-import Types.FileMatcher
-import qualified Limit
-
--- a named computation that produces a statistic
-type Stat = StatState (Maybe (String, StatState String))
-
--- data about a set of keys
-data KeyData = KeyData
-	{ countKeys :: Integer
-	, sizeKeys :: Integer
-	, unknownSizeKeys :: Integer
-	, backendsKeys :: M.Map String Integer
-	}
-
-data NumCopiesStats = NumCopiesStats
-	{ numCopiesVarianceMap :: M.Map Variance Integer
-	}
-
-newtype Variance = Variance Int
-	deriving (Eq, Ord)
-
-instance Show Variance where
-	show (Variance n)
-		| n >= 0 = "numcopies +" ++ show n
-		| otherwise = "numcopies " ++ show n
-
--- cached info that multiple Stats use
-data StatInfo = StatInfo
-	{ presentData :: Maybe KeyData
-	, referencedData :: Maybe KeyData
-	, numCopiesStats :: Maybe NumCopiesStats
-	}
-
--- a state monad for running Stats in
-type StatState = StateT StatInfo Annex
+import qualified Git.LsFiles as LsFiles
+import qualified Git.Ref
+import qualified Git
 
 def :: [Command]
-def = [noCommit $ command "status" paramPaths seek
-	SectionQuery "shows status information about the annex"]
+def = [notBareRepo $ noCommit $ noMessages $
+	command "status" paramPaths seek SectionCommon
+		"show the working tree status"]
 
 seek :: [CommandSeek]
-seek = [withWords start]
+seek = 
+	[ withWords start
+	]
 
 start :: [FilePath] -> CommandStart
 start [] = do
-	globalStatus
-	stop
-start ps = do
-	mapM_ localStatus =<< filterM isdir ps
-	stop
-  where
-	isdir = liftIO . catchBoolIO . (isDirectory <$$> getFileStatus)
-
-globalStatus :: Annex ()
-globalStatus = do
-	stats <- selStats global_fast_stats global_slow_stats
-	showCustom "status" $ do
-		evalStateT (mapM_ showStat stats) (StatInfo Nothing Nothing Nothing)
-		return True
-
-localStatus :: FilePath -> Annex ()
-localStatus dir = showCustom (unwords ["status", dir]) $ do
-	stats <- selStats (tostats local_fast_stats) (tostats local_slow_stats)
-	evalStateT (mapM_ showStat stats) =<< getLocalStatInfo dir
-	return True
-  where
-  	tostats = map (\s -> s dir)
-
-selStats :: [Stat] -> [Stat] -> Annex [Stat]
-selStats fast_stats slow_stats = do
-	fast <- Annex.getState Annex.fast
-	return $ if fast
-		then fast_stats
-		else fast_stats ++ slow_stats
-
-{- Order is significant. Less expensive operations, and operations
- - that share data go together.
- -}
-global_fast_stats :: [Stat]
-global_fast_stats = 
-	[ repository_mode
-	, remote_list Trusted
-	, remote_list SemiTrusted
-	, remote_list UnTrusted
-	, transfer_list
-	, disk_size
-	]
-global_slow_stats :: [Stat]
-global_slow_stats = 
-	[ tmp_size
-	, bad_data_size
-	, local_annex_keys
-	, local_annex_size
-	, known_annex_files
-	, known_annex_size
-	, bloom_info
-	, backend_usage
-	]
-local_fast_stats :: [FilePath -> Stat]
-local_fast_stats =
-	[ local_dir
-	, const local_annex_keys
-	, const local_annex_size
-	, const known_annex_files
-	, const known_annex_size
-	]
-local_slow_stats :: [FilePath -> Stat]
-local_slow_stats =
-	[ const numcopies_stats
-	]
-
-stat :: String -> (String -> StatState String) -> Stat
-stat desc a = return $ Just (desc, a desc)
-
-nostat :: Stat
-nostat = return Nothing
-
-json :: JSON j => (j -> String) -> StatState j -> String -> StatState String
-json serialize a desc = do
-	j <- a
-	lift $ maybeShowJSON [(desc, j)]
-	return $ serialize j
-
-nojson :: StatState String -> String -> StatState String
-nojson a _ = a
-
-showStat :: Stat -> StatState ()
-showStat s = maybe noop calc =<< s
-  where
-	calc (desc, a) = do
-		(lift . showHeader) desc
-		lift . showRaw =<< a
-
-repository_mode :: Stat
-repository_mode = stat "repository mode" $ json id $ lift $
-	ifM isDirect 
-		( return "direct", return "indirect" )
-
-remote_list :: TrustLevel -> Stat
-remote_list level = stat n $ nojson $ lift $ do
-	us <- M.keys <$> (M.union <$> uuidMap <*> remoteMap Remote.name)
-	rs <- fst <$> trustPartition level us
-	s <- prettyPrintUUIDs n rs
-	return $ if null s then "0" else show (length rs) ++ "\n" ++ beginning s
-  where
-	n = showTrustLevel level ++ " repositories"
+	-- Like git status, when run without a directory, behave as if
+	-- given the path to the top of the repository.
+	cwd <- liftIO getCurrentDirectory
+	top <- fromRepo Git.repoPath
+	next $ perform [relPathDirToFile cwd top]
+start locs = next $ perform locs
 	
-local_dir :: FilePath -> Stat
-local_dir dir = stat "directory" $ json id $ return dir
-
-local_annex_keys :: Stat
-local_annex_keys = stat "local annex keys" $ json show $
-	countKeys <$> cachedPresentData
-
-local_annex_size :: Stat
-local_annex_size = stat "local annex size" $ json id $
-	showSizeKeys <$> cachedPresentData
-
-known_annex_files :: Stat
-known_annex_files = stat "annexed files in working tree" $ json show $
-	countKeys <$> cachedReferencedData
-
-known_annex_size :: Stat
-known_annex_size = stat "size of annexed files in working tree" $ json id $
-	showSizeKeys <$> cachedReferencedData
-
-tmp_size :: Stat
-tmp_size = staleSize "temporary directory size" gitAnnexTmpDir
-
-bad_data_size :: Stat
-bad_data_size = staleSize "bad keys size" gitAnnexBadDir
-
-bloom_info :: Stat
-bloom_info = stat "bloom filter size" $ json id $ do
-	localkeys <- countKeys <$> cachedPresentData
-	capacity <- fromIntegral <$> lift Command.Unused.bloomCapacity
-	let note = aside $
-		if localkeys >= capacity
-		then "appears too small for this repository; adjust annex.bloomcapacity"
-		else showPercentage 1 (percentage capacity localkeys) ++ " full"
-
-	-- Two bloom filters are used at the same time, so double the size
-	-- of one.
-	size <- roughSize memoryUnits False . (* 2) . fromIntegral . fst <$>
-		lift Command.Unused.bloomBitsHashes
-
-	return $ size ++ note
-
-transfer_list :: Stat
-transfer_list = stat "transfers in progress" $ nojson $ lift $ do
-	uuidmap <- Remote.remoteMap id
-	ts <- getTransfers
-	return $ if null ts
-		then "none"
-		else multiLine $
-			map (uncurry $ line uuidmap) $ sort ts
-  where
-	line uuidmap t i = unwords
-		[ showLcDirection (transferDirection t) ++ "ing"
-		, fromMaybe (key2file $ transferKey t) (associatedFile i)
-		, if transferDirection t == Upload then "to" else "from"
-		, maybe (fromUUID $ transferUUID t) Remote.name $
-			M.lookup (transferUUID t) uuidmap
-		]
-
-disk_size :: Stat
-disk_size = stat "available local disk space" $ json id $ lift $
-	calcfree
-		<$> (annexDiskReserve <$> Annex.getGitConfig)
-		<*> inRepo (getDiskFree . gitAnnexDir)
-  where
-	calcfree reserve (Just have) = unwords
-		[ roughSize storageUnits False $ nonneg $ have - reserve
-		, "(+" ++ roughSize storageUnits False reserve
-		, "reserved)"
-		]			
-	calcfree _ _ = "unknown"
-
-	nonneg x
-		| x >= 0 = x
-		| otherwise = 0
-
-backend_usage :: Stat
-backend_usage = stat "backend usage" $ nojson $
-	calc
-		<$> (backendsKeys <$> cachedReferencedData)
-		<*> (backendsKeys <$> cachedPresentData)
-  where
-	calc x y = multiLine $
-		map (\(n, b) -> b ++ ": " ++ show n) $
-		reverse $ sort $ map swap $ M.toList $
-		M.unionWith (+) x y
-
-numcopies_stats :: Stat
-numcopies_stats = stat "numcopies stats" $ nojson $
-	calc <$> (maybe M.empty numCopiesVarianceMap <$> cachedNumCopiesStats)
+perform :: [FilePath] -> CommandPerform
+perform locs = do
+	(l, cleanup) <- inRepo $ LsFiles.modifiedOthers locs
+	getstatus <- ifM isDirect
+		( return statusDirect
+		, return $ Just <$$> statusIndirect
+		)
+	forM_ l $ \f -> maybe noop (showFileStatus f) =<< getstatus f
+	void $ liftIO cleanup
+	next $ return True
+
+data Status 
+	= NewFile
+	| DeletedFile
+	| ModifiedFile
+
+showStatus :: Status -> String
+showStatus NewFile = "?"
+showStatus DeletedFile = "D"
+showStatus ModifiedFile = "M"
+
+showFileStatus :: FilePath -> Status -> Annex ()
+showFileStatus f s  = liftIO $ putStrLn $ showStatus s ++ " " ++ f
+
+statusDirect :: FilePath -> Annex (Maybe Status)
+statusDirect f = checkstatus =<< liftIO (catchMaybeIO $ getFileStatus f)
   where
-	calc = multiLine
-		. map (\(variance, count) -> show variance ++ ": " ++ show count)
-		. reverse . sortBy (comparing snd) . M.toList
-
-cachedPresentData :: StatState KeyData
-cachedPresentData = do
-	s <- get
-	case presentData s of
-		Just v -> return v
-		Nothing -> do
-			v <- foldKeys <$> lift getKeysPresent
-			put s { presentData = Just v }
-			return v
-
-cachedReferencedData :: StatState KeyData
-cachedReferencedData = do
-	s <- get
-	case referencedData s of
-		Just v -> return v
-		Nothing -> do
-			!v <- lift $ Command.Unused.withKeysReferenced
-				emptyKeyData addKey
-			put s { referencedData = Just v }
-			return v
-
--- currently only available for local status
-cachedNumCopiesStats :: StatState (Maybe NumCopiesStats)
-cachedNumCopiesStats = numCopiesStats <$> get
-
-getLocalStatInfo :: FilePath -> Annex StatInfo
-getLocalStatInfo dir = do
-	fast <- Annex.getState Annex.fast
-	matcher <- Limit.getMatcher
-	(presentdata, referenceddata, numcopiesstats) <-
-		Command.Unused.withKeysFilesReferencedIn dir initial
-			(update matcher fast)
-	return $ StatInfo (Just presentdata) (Just referenceddata) (Just numcopiesstats)
-  where
-	initial = (emptyKeyData, emptyKeyData, emptyNumCopiesStats)
-	update matcher fast key file vs@(presentdata, referenceddata, numcopiesstats) =
-		ifM (matcher $ FileInfo file file)
-			( do
-				!presentdata' <- ifM (inAnnex key)
-					( return $ addKey key presentdata
-					, return presentdata
-					)
-				let !referenceddata' = addKey key referenceddata
-				!numcopiesstats' <- if fast
-					then return numcopiesstats
-					else updateNumCopiesStats key file numcopiesstats
-				return $! (presentdata', referenceddata', numcopiesstats')
-			, return vs
-			)
-
-emptyKeyData :: KeyData
-emptyKeyData = KeyData 0 0 0 M.empty
-
-emptyNumCopiesStats :: NumCopiesStats
-emptyNumCopiesStats = NumCopiesStats M.empty
-
-foldKeys :: [Key] -> KeyData
-foldKeys = foldl' (flip addKey) emptyKeyData
-
-addKey :: Key -> KeyData -> KeyData
-addKey key (KeyData count size unknownsize backends) =
-	KeyData count' size' unknownsize' backends'
-  where
-	{- All calculations strict to avoid thunks when repeatedly
-	 - applied to many keys. -}
-	!count' = count + 1
-	!backends' = M.insertWith' (+) (keyBackendName key) 1 backends
-	!size' = maybe size (+ size) ks
-	!unknownsize' = maybe (unknownsize + 1) (const unknownsize) ks
-	ks = keySize key
-
-updateNumCopiesStats :: Key -> FilePath -> NumCopiesStats -> Annex NumCopiesStats
-updateNumCopiesStats key file (NumCopiesStats m) = do
-	!variance <- Variance <$> numCopiesCheck file key (-)
-	let !m' = M.insertWith' (+) variance 1 m
-	let !ret = NumCopiesStats m'
-	return ret
-
-showSizeKeys :: KeyData -> String
-showSizeKeys d = total ++ missingnote
-  where
-	total = roughSize storageUnits False $ sizeKeys d
-	missingnote
-		| unknownSizeKeys d == 0 = ""
-		| otherwise = aside $
-			"+ " ++ show (unknownSizeKeys d) ++
-			" unknown size"
-
-staleSize :: String -> (Git.Repo -> FilePath) -> Stat
-staleSize label dirspec = go =<< lift (dirKeys dirspec)
+	checkstatus Nothing = return $ Just DeletedFile
+	checkstatus (Just s)
+		-- Git thinks that present direct mode files modifed,
+		-- so have to check.
+		| not (isSymbolicLink s) = checkkey s =<< catKeyFile f
+		| otherwise = Just <$> checkNew f
+	
+	checkkey s (Just k) = ifM (sameFileStatus k s)
+		( return Nothing
+		, return $ Just ModifiedFile
+		)
+	checkkey _ Nothing = Just <$> checkNew f
+
+statusIndirect :: FilePath -> Annex Status
+statusIndirect f = ifM (liftIO $ isJust <$> catchMaybeIO (getFileStatus f))
+	( checkNew f
+	, return DeletedFile
+	)
   where
-	go [] = nostat
-	go keys = onsize =<< sum <$> keysizes keys
-	onsize 0 = nostat
-	onsize size = stat label $
-		json (++ aside "clean up with git-annex unused") $
-			return $ roughSize storageUnits False size
-	keysizes keys = do
-		dir <- lift $ fromRepo dirspec
-		liftIO $ forM keys $ \k -> catchDefaultIO 0 $
-			fromIntegral . fileSize 
-				<$> getFileStatus (dir </> keyFile k)
-
-aside :: String -> String
-aside s = " (" ++ s ++ ")"
 
-multiLine :: [String] -> String
-multiLine = concatMap (\l -> "\n\t" ++ l)
+checkNew :: FilePath -> Annex Status
+checkNew f = ifM (isJust <$> catObjectDetails (Git.Ref.fileRef f))
+	( return ModifiedFile
+	, return NewFile
+	)
diff --git a/Command/Sync.hs b/Command/Sync.hs
index 1fbd9c028..c41f46f8a 100644
--- a/Command/Sync.hs
+++ b/Command/Sync.hs
@@ -45,13 +45,15 @@ seek rs = do
 	prepMerge
 
 	-- There may not be a branch checked out until after the commit,
-	-- so only look it up once needed, and only look it up once.
+	-- or perhaps after it gets merged from the remote.
+	-- So only look it up once it's needed, and if once there is a
+	-- branch, cache it.
 	mvar <- liftIO newEmptyMVar
 	let getbranch = ifM (liftIO $ isEmptyMVar mvar)
 		( do
-			branch <- fromMaybe (error "no branch is checked out")
-				<$> inRepo Git.Branch.current
-			liftIO $ putMVar mvar branch
+			branch <- inRepo Git.Branch.current
+			when (isJust branch) $
+				liftIO $ putMVar mvar branch
 			return branch
 		, liftIO $ readMVar mvar
 		)
@@ -73,10 +75,10 @@ prepMerge :: Annex ()
 prepMerge = liftIO . setCurrentDirectory =<< fromRepo Git.repoPath
 
 syncBranch :: Git.Ref -> Git.Ref
-syncBranch = Git.Ref.under "refs/heads/synced/"
+syncBranch = Git.Ref.under "refs/heads/synced" . fromDirectBranch
 
 remoteBranch :: Remote -> Git.Ref -> Git.Ref
-remoteBranch remote = Git.Ref.under $ "refs/remotes/" ++ Remote.name remote
+remoteBranch remote = Git.Ref.underBase $ "refs/remotes/" ++ Remote.name remote
 
 syncRemotes :: [String] -> Annex [Remote]
 syncRemotes rs = ifM (Annex.getState Annex.fast) ( nub <$> pickfast , wanted )
@@ -116,8 +118,9 @@ commit = next $ next $ ifM isDirect
 		_ <- inRepo $ tryIO . Git.Command.runQuiet params
 		return True
 
-mergeLocal :: Git.Ref -> CommandStart
-mergeLocal branch = go =<< needmerge
+mergeLocal :: Maybe Git.Ref -> CommandStart
+mergeLocal Nothing = stop
+mergeLocal (Just branch) = go =<< needmerge
   where
 	syncbranch = syncBranch branch
 	needmerge = ifM isBareRepo
@@ -132,9 +135,16 @@ mergeLocal branch = go =<< needmerge
 		showStart "merge" $ Git.Ref.describe syncbranch
 		next $ next $ mergeFrom syncbranch
 
-pushLocal :: Git.Ref -> CommandStart
-pushLocal branch = do
+pushLocal :: Maybe Git.Ref -> CommandStart
+pushLocal Nothing = stop
+pushLocal (Just branch) = do
+	-- Update the sync branch to match the new state of the branch
 	inRepo $ updateBranch $ syncBranch branch
+	-- In direct mode, we're operating on some special direct mode
+	-- branch, rather than the intended branch, so update the indended
+	-- branch.
+	whenM isDirect $
+		inRepo $ updateBranch $ fromDirectBranch branch
 	stop
 
 updateBranch :: Git.Ref -> Git.Repo -> IO ()
@@ -147,13 +157,13 @@ updateBranch syncbranch g =
 		, Param $ show $ Git.Ref.base syncbranch
 		] g
 
-pullRemote :: Remote -> Git.Ref -> CommandStart
+pullRemote :: Remote -> Maybe Git.Ref -> CommandStart
 pullRemote remote branch = do
 	showStart "pull" (Remote.name remote)
 	next $ do
 		showOutput
 		stopUnless fetch $
-			next $ mergeRemote remote (Just branch)
+			next $ mergeRemote remote branch
   where
 	fetch = inRepo $ Git.Command.runBool
 		[Param "fetch", Param $ Remote.name remote]
@@ -175,8 +185,9 @@ mergeRemote remote b = case b of
 	branchlist Nothing = []
 	branchlist (Just branch) = [branch, syncBranch branch]
 
-pushRemote :: Remote -> Git.Ref -> CommandStart
-pushRemote remote branch = go =<< needpush
+pushRemote :: Remote -> Maybe Git.Ref -> CommandStart
+pushRemote _remote Nothing = stop
+pushRemote remote (Just branch) = go =<< needpush
   where
 	needpush = anyM (newer remote) [syncBranch branch, Annex.Branch.name]
 	go False = stop
@@ -227,7 +238,7 @@ pushBranch remote branch g = tryIO (directpush g) `after` syncpush g
 		, refspec branch
 		]
 	directpush = Git.Command.runQuiet $ pushparams
-		[show $ Git.Ref.base branch]
+		[show $ Git.Ref.base $ fromDirectBranch branch]
 	pushparams branches =
 		[ Param "push"
 		, Param $ Remote.name remote
@@ -310,6 +321,7 @@ resolveMerge = do
 			, Param "-m"
 			, Param "git-annex automatic merge conflict fix"
 			]
+		showLongNote "Merge conflict was automatically resolved; you may want to examine the result."
 	return merged
 
 resolveMerge' :: LsFiles.Unmerged -> Annex (Maybe FilePath)
diff --git a/Command/TransferKey.hs b/Command/TransferKey.hs
index 3270ad8f7..5bb53d98d 100644
--- a/Command/TransferKey.hs
+++ b/Command/TransferKey.hs
@@ -56,4 +56,4 @@ fromPerform remote key file = go $
 		getViaTmp key $ \t -> Remote.retrieveKeyFile remote key file t p
 
 go :: Annex Bool -> CommandPerform
-go a = ifM a ( liftIO exitSuccess,  liftIO exitFailure)
+go a = a >>= liftIO . exitBool
diff --git a/Command/Unused.hs b/Command/Unused.hs
index 844cdb19b..1e5cdc163 100644
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -332,11 +332,13 @@ withUnusedMaps a params = do
 	unused <- readUnusedLog ""
 	unusedbad <- readUnusedLog "bad"
 	unusedtmp <- readUnusedLog "tmp"
+	let m = unused `M.union` unusedbad `M.union` unusedtmp
 	return $ map (a $ UnusedMaps unused unusedbad unusedtmp) $
-		concatMap unusedSpec params
+		concatMap (unusedSpec m) params
 
-unusedSpec :: String -> [Int]
-unusedSpec spec
+unusedSpec :: UnusedMap -> String -> [Int]
+unusedSpec m spec
+	| spec == "all" = [fst (M.findMin m)..fst (M.findMax m)]
 	| "-" `isInfixOf` spec = range $ separate (== '-') spec
 	| otherwise = maybe badspec (: []) (readish spec)
   where
diff --git a/Command/Upgrade.hs b/Command/Upgrade.hs
index 88ca8622d..c6c0f7a8c 100644
--- a/Command/Upgrade.hs
+++ b/Command/Upgrade.hs
@@ -11,6 +11,7 @@ import Common.Annex
 import Command
 import Upgrade
 import Annex.Version
+import Config
 
 def :: [Command]
 def = [dontCheck repoExists $ -- because an old version may not seem to exist
@@ -23,6 +24,5 @@ seek = [withNothing start]
 start :: CommandStart
 start = do
 	showStart "upgrade" "."
-	r <- upgrade
-	setVersion defaultVersion
+	r <- upgrade False
 	next $ next $ return r
diff --git a/Command/Watch.hs b/Command/Watch.hs
index 0b34b0f84..a33fc633c 100644
--- a/Command/Watch.hs
+++ b/Command/Watch.hs
@@ -32,5 +32,5 @@ start :: Bool -> Bool -> Bool -> Maybe Duration -> CommandStart
 start assistant foreground stopdaemon startdelay = do
 	if stopdaemon
 		then stopDaemon
-		else startDaemon assistant foreground startdelay Nothing Nothing -- does not return
+		else startDaemon assistant foreground startdelay Nothing Nothing Nothing -- does not return
 	stop
diff --git a/Command/WebApp.hs b/Command/WebApp.hs
index 88c1537d0..70f28a113 100644
--- a/Command/WebApp.hs
+++ b/Command/WebApp.hs
@@ -30,6 +30,8 @@ import qualified Git.CurrentRepo
 import qualified Annex
 import Config.Files
 import qualified Option
+import Upgrade
+import Annex.Version
 
 import Control.Concurrent
 import Control.Concurrent.STM
@@ -56,10 +58,14 @@ start = start' True
 start' :: Bool -> Maybe HostName -> CommandStart
 start' allowauto listenhost = do
 	liftIO ensureInstalled
-	ifM isInitialized ( go , auto )
+	ifM isInitialized 
+		( go
+		, auto
+		)
 	stop
   where
 	go = do
+		cannotrun <- needsUpgrade . fromMaybe (error "no version") =<< getVersion
 		browser <- fromRepo webBrowser
 		f <- liftIO . absPath =<< fromRepo gitAnnexHtmlShim
 		ifM (checkpid <&&> checkshim f)
@@ -69,7 +75,7 @@ start' allowauto listenhost = do
 					url <- liftIO . readFile
 						=<< fromRepo gitAnnexUrlFile
 					liftIO $ openBrowser browser f url Nothing Nothing
-			, startDaemon True True Nothing listenhost $ Just $ 
+			, startDaemon True True Nothing cannotrun listenhost $ Just $ 
 				\origout origerr url htmlshim ->
 					if isJust listenhost
 						then maybe noop (`hPutStrLn` url) origout
@@ -133,7 +139,7 @@ firstRun listenhost = do
 	let callback a = Just $ a v
 	runAssistant d $ do
 		startNamedThread urlrenderer $
-			webAppThread d urlrenderer True listenhost
+			webAppThread d urlrenderer True Nothing listenhost
 				(callback signaler)
 				(callback mainthread)
 		waitNamedThreads
@@ -155,7 +161,7 @@ firstRun listenhost = do
 			_wait <- takeMVar v
 			state <- Annex.new =<< Git.CurrentRepo.get
 			Annex.eval state $
-				startDaemon True True Nothing listenhost $ Just $
+				startDaemon True True Nothing Nothing listenhost $ Just $
 					sendurlback v
 	sendurlback v _origout _origerr url _htmlshim = do
 		recordUrl url
diff --git a/Config.hs b/Config.hs
index ac251983a..0c6b64f50 100644
--- a/Config.hs
+++ b/Config.hs
@@ -71,11 +71,6 @@ getNumCopies Nothing = annexNumCopies <$> Annex.getGitConfig
 isDirect :: Annex Bool
 isDirect = annexDirect <$> Annex.getGitConfig
 
-setDirect :: Bool -> Annex ()
-setDirect b = do
-	setConfig (annexConfig "direct") (Git.Config.boolConfig b)
-	Annex.changeGitConfig $ \c -> c { annexDirect = b }
-
 crippledFileSystem :: Annex Bool
 crippledFileSystem = annexCrippledFileSystem <$> Annex.getGitConfig
 
diff --git a/Git/Branch.hs b/Git/Branch.hs
index 01d028f55..7b3297d74 100644
--- a/Git/Branch.hs
+++ b/Git/Branch.hs
@@ -13,7 +13,7 @@ import Common
 import Git
 import Git.Sha
 import Git.Command
-import Git.Ref (headRef)
+import qualified Git.Ref
 
 {- The currently checked out branch.
  -
@@ -36,7 +36,7 @@ current r = do
 {- The current branch, which may not really exist yet. -}
 currentUnsafe :: Repo -> IO (Maybe Git.Ref)
 currentUnsafe r = parse . firstLine
-	<$> pipeReadStrict [Param "symbolic-ref", Param $ show headRef] r
+	<$> pipeReadStrict [Param "symbolic-ref", Param $ show Git.Ref.headRef] r
   where
 	parse l
 		| null l = Nothing
@@ -97,7 +97,7 @@ commit message branch parentrefs repo = do
 	sha <- getSha "commit-tree" $ pipeWriteRead
 		(map Param $ ["commit-tree", show tree] ++ ps)
 		(Just $ flip hPutStr message) repo
-	run [Param "update-ref", Param $ show branch, Param $ show sha] repo
+	update branch sha repo
 	return sha
   where
 	ps = concatMap (\r -> ["-p", show r]) parentrefs
@@ -105,3 +105,29 @@ commit message branch parentrefs repo = do
 {- A leading + makes git-push force pushing a branch. -}
 forcePush :: String -> String
 forcePush b = "+" ++ b
+
+{- Updates a branch (or other ref) to a new Sha. -}
+update :: Branch -> Sha -> Repo -> IO ()
+update branch sha = run 
+	[ Param "update-ref"
+	, Param $ show branch
+	, Param $ show sha
+	]
+
+{- Checks out a branch, creating it if necessary. -}
+checkout :: Branch -> Repo -> IO ()
+checkout branch = run
+	[ Param "checkout"
+	, Param "-q"
+	, Param "-B"
+	, Param $ show $ Git.Ref.base branch
+	]
+
+{- Removes a branch. -}
+delete :: Branch -> Repo -> IO ()
+delete branch = run
+	[ Param "branch"
+	, Param "-q"
+	, Param "-D"
+	, Param $ show $ Git.Ref.base branch
+	]
diff --git a/Git/Command.hs b/Git/Command.hs
index 8b027d2c3..adcc53bcd 100644
--- a/Git/Command.hs
+++ b/Git/Command.hs
@@ -21,7 +21,8 @@ import Git.FilePath
 
 {- Constructs a git command line operating on the specified repo. -}
 gitCommandLine :: [CommandParam] -> Repo -> [CommandParam]
-gitCommandLine params Repo { location = l@(Local _ _ ) } = setdir : settree ++ params
+gitCommandLine params r@(Repo { location = l@(Local _ _ ) }) =
+	setdir : settree ++ gitGlobalOpts r ++ params
   where
 	setdir = Param $ "--git-dir=" ++ gitpath (gitdir l)
 	settree = case worktree l of
diff --git a/Git/Config.hs b/Git/Config.hs
index a41712add..b5c1be04a 100644
--- a/Git/Config.hs
+++ b/Git/Config.hs
@@ -110,8 +110,13 @@ store s repo = do
  -}
 updateLocation :: Repo -> IO Repo
 updateLocation r@(Repo { location = LocalUnknown d })
-	| isBare r = updateLocation' r $ Local d Nothing
-	| otherwise = updateLocation' r $ Local (d </> ".git") (Just d)
+	| isBare r = ifM (doesDirectoryExist dotgit)
+			( updateLocation' r $ Local dotgit Nothing
+			, updateLocation' r $ Local d Nothing
+			)
+	| otherwise = updateLocation' r $ Local dotgit (Just d)
+  where
+	dotgit = (d </> ".git")
 updateLocation r@(Repo { location = l@(Local {}) }) = updateLocation' r l
 updateLocation r = return r
 
@@ -153,7 +158,10 @@ boolConfig True = "true"
 boolConfig False = "false"
 
 isBare :: Repo -> Bool
-isBare r = fromMaybe False $ isTrue =<< getMaybe "core.bare" r
+isBare r = fromMaybe False $ isTrue =<< getMaybe coreBare r
+
+coreBare :: String
+coreBare = "core.bare"
 
 {- Runs a command to get the configuration of a repo,
  - and returns a repo populated with the configuration, as well as the raw
diff --git a/Git/Construct.hs b/Git/Construct.hs
index 6514b80bc..71a13f49f 100644
--- a/Git/Construct.hs
+++ b/Git/Construct.hs
@@ -104,14 +104,16 @@ localToUrl :: Repo -> Repo -> Repo
 localToUrl reference r
 	| not $ repoIsUrl reference = error "internal error; reference repo not url"
 	| repoIsUrl r = r
-	| otherwise = r { location = Url $ fromJust $ parseURI absurl }
-  where
-	absurl = concat
-		[ Url.scheme reference
-		, "//"
-		, Url.authority reference
-		, repoPath r
-		]
+	| otherwise = case Url.authority reference of
+		Nothing -> r
+		Just auth -> 
+			let absurl = concat
+				[ Url.scheme reference
+				, "//"
+				, auth
+				, repoPath r
+				]
+			in r { location = Url $ fromJust $ parseURI absurl }
 
 {- Calculates a list of a repo's configured remotes, by parsing its config. -}
 fromRemotes :: Repo -> IO [Repo]
@@ -228,6 +230,7 @@ newFrom l = return Repo
 	, remotes = []
 	, remoteName = Nothing
 	, gitEnv = Nothing
+	, gitGlobalOpts = []
 	}
 
 
diff --git a/Git/Fsck.hs b/Git/Fsck.hs
index 2c9423005..8bfddb4ba 100644
--- a/Git/Fsck.hs
+++ b/Git/Fsck.hs
@@ -17,7 +17,6 @@ import Common
 import Git
 import Git.Command
 import Git.Sha
-import Git.CatFile
 import Utility.Batch
 
 import qualified Data.Set as S
@@ -40,7 +39,7 @@ type FsckResults = Maybe MissingObjects
 findBroken :: Bool -> Repo -> IO FsckResults
 findBroken batchmode r = do
 	(output, fsckok) <- processTranscript command' (toCommand params') Nothing
-	let objs = parseFsckOutput output
+	let objs = findShas output
 	badobjs <- findMissing objs r
 	if S.null badobjs && not fsckok
 		then return Nothing
@@ -57,30 +56,23 @@ foundBroken (Just s) = not (S.null s)
 
 {- Finds objects that are missing from the git repsitory, or are corrupt.
  -
- - Note that catting a corrupt object will cause cat-file to crash;
- - this is detected and it's restarted.
+ - This does not use git cat-file --batch, because catting a corrupt
+ - object can cause it to crash, or to report incorrect size information.a
  -}
 findMissing :: [Sha] -> Repo -> IO MissingObjects
-findMissing objs r = go objs [] =<< start
+findMissing objs r = S.fromList <$> filterM (not <$$> present) objs
   where
-	start = catFileStart' False r
-	go [] c h = do
-		catFileStop h
-		return $ S.fromList c
-	go (o:os) c h = do
-		v <- tryIO $ isNothing <$> catObjectDetails h o
-		case v of
-			Left _ -> do
-				void $ tryIO $ catFileStop h
-				go os (o:c) =<< start
-			Right True -> go os (o:c) h
-			Right False -> go os c h
+	present o = either (const False) (const True) <$> tryIO (dump o)
+	dump o = runQuiet
+		[ Param "show"
+		, Param (show o)
+		] r
 
-parseFsckOutput :: String -> [Sha]
-parseFsckOutput = catMaybes . map extractSha . concat . map words . lines
+findShas :: String -> [Sha]
+findShas = catMaybes . map extractSha . concat . map words . lines
 
 fsckParams :: Repo -> [CommandParam]
-fsckParams = gitCommandLine
+fsckParams = gitCommandLine $
 	[ Param "fsck"
 	, Param "--no-dangling"
 	, Param "--no-reflogs"
diff --git a/Git/GCrypt.hs b/Git/GCrypt.hs
index 0da68bf24..156441dae 100644
--- a/Git/GCrypt.hs
+++ b/Git/GCrypt.hs
@@ -15,7 +15,6 @@ import Git.Construct
 import qualified Git.Config as Config
 import qualified Git.Command as Command
 import Utility.Gpg
-import Git.Remote
 
 urlPrefix :: String
 urlPrefix = "gcrypt::"
diff --git a/Git/Hook.hs b/Git/Hook.hs
new file mode 100644
index 000000000..d56a4a565
--- /dev/null
+++ b/Git/Hook.hs
@@ -0,0 +1,54 @@
+{- git hooks
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Git.Hook where
+
+import Common
+import Git
+import Utility.Tmp
+
+data Hook = Hook
+	{ hookName :: FilePath
+	, hookScript :: String
+	}
+
+hookFile :: Hook -> Repo -> FilePath
+hookFile h r = localGitDir r </> "hooks" </> hookName h
+
+{- Writes a hook. Returns False if the hook already exists with a different
+ - content. -}
+hookWrite :: Hook -> Repo -> IO Bool
+hookWrite h r = do
+	let f = hookFile h r
+	ifM (doesFileExist f)
+		( expectedContent h r
+		, do
+			viaTmp writeFile f (hookScript h)
+			p <- getPermissions f
+			setPermissions f $ p {executable = True}
+			return True
+		)
+
+{- Removes a hook. Returns False if the hook contained something else, and
+ - could not be removed. -}
+hookUnWrite :: Hook -> Repo -> IO Bool
+hookUnWrite h r = do
+	let f = hookFile h r
+	ifM (doesFileExist f)
+		( ifM (expectedContent h r)
+			( do
+				removeFile f
+				return True
+			, return False
+			)
+		, return True
+		)
+
+expectedContent :: Hook -> Repo -> IO Bool
+expectedContent h r = do
+	content <- readFile $ hookFile h r
+	return $ content == hookScript h
diff --git a/Git/LsFiles.hs b/Git/LsFiles.hs
index 98cbac58e..8aaa09067 100644
--- a/Git/LsFiles.hs
+++ b/Git/LsFiles.hs
@@ -11,6 +11,7 @@ module Git.LsFiles (
 	allFiles,
 	deleted,
 	modified,
+	modifiedOthers,
 	staged,
 	stagedNotDeleted,
 	stagedOthersDetails,
@@ -65,6 +66,12 @@ modified l repo = pipeNullSplit params repo
   where
 	params = [Params "ls-files --modified -z --"] ++ map File l
 
+{- Files that have been modified or are not checked into git. -}
+modifiedOthers :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+modifiedOthers l repo = pipeNullSplit params repo
+  where
+	params = [Params "ls-files --modified --others -z --"] ++ map File l
+
 {- Returns a list of all files that are staged for commit. -}
 staged :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)
 staged = staged' []
diff --git a/Git/Objects.hs b/Git/Objects.hs
index b1c580533..d9d2c6701 100644
--- a/Git/Objects.hs
+++ b/Git/Objects.hs
@@ -9,6 +9,7 @@ module Git.Objects where
 
 import Common
 import Git
+import Git.Sha
 
 objectsDir :: Repo -> FilePath
 objectsDir r = localGitDir r </> "objects"
@@ -16,12 +17,17 @@ objectsDir r = localGitDir r </> "objects"
 packDir :: Repo -> FilePath
 packDir r = objectsDir r </> "pack"
 
+packIdxFile :: FilePath -> FilePath
+packIdxFile = flip replaceExtension "idx"
+
 listPackFiles :: Repo -> IO [FilePath]
 listPackFiles r = filter (".pack" `isSuffixOf`) 
 	<$> catchDefaultIO [] (dirContents $ packDir r)
 
-packIdxFile :: FilePath -> FilePath
-packIdxFile = flip replaceExtension "idx"
+listLooseObjectShas :: Repo -> IO [Sha]
+listLooseObjectShas r = catchDefaultIO [] $
+	mapMaybe (extractSha . concat . reverse . take 2 . reverse . splitDirectories)
+		<$> dirContentsRecursiveSkipping (== "pack") (objectsDir r)
 
 looseObjectFile :: Repo -> Sha -> FilePath
 looseObjectFile r sha = objectsDir r </> prefix </> rest
diff --git a/Git/Ref.hs b/Git/Ref.hs
index 954b61a2e..6ce1b8784 100644
--- a/Git/Ref.hs
+++ b/Git/Ref.hs
@@ -29,17 +29,42 @@ base = Ref . remove "refs/heads/" . remove "refs/remotes/" . show
 		| prefix `isPrefixOf` s = drop (length prefix) s
 		| otherwise = s
 
+{- Given a directory and any ref, takes the basename of the ref and puts
+ - it under the directory. -}
+under :: String -> Ref -> Ref
+under dir r = Ref $ dir ++ "/" ++
+	(reverse $ takeWhile (/= '/') $ reverse $ show r)
+
 {- Given a directory such as "refs/remotes/origin", and a ref such as
  - refs/heads/master, yields a version of that ref under the directory,
  - such as refs/remotes/origin/master. -}
-under :: String -> Ref -> Ref
-under dir r = Ref $ dir </> show (base r)
+underBase :: String -> Ref -> Ref
+underBase dir r = Ref $ dir ++ "/" ++ show (base r)
+
+{- A Ref that can be used to refer to a file in the repository, as staged
+ - in the index.
+ -
+ - Prefixing the file with ./ makes this work even if in a subdirectory
+ - of a repo.
+ -}
+fileRef :: FilePath -> Ref
+fileRef f = Ref $ ":./" ++ f
+
+{- A Ref that can be used to refer to a file in the repository as it
+ - appears in a given Ref. -}
+fileFromRef :: Ref -> FilePath -> Ref
+fileFromRef (Ref r) f = let (Ref fr) = fileRef f in Ref (r ++ fr)
 
 {- Checks if a ref exists. -}
 exists :: Ref -> Repo -> IO Bool
 exists ref = runBool
 	[Param "show-ref", Param "--verify", Param "-q", Param $ show ref]
 
+{- The file used to record a ref. (Git also stores some refs in a
+ - packed-refs file.) -}
+file :: Ref -> Repo -> FilePath
+file ref repo = localGitDir repo </> show ref
+
 {- Checks if HEAD exists. It generally will, except for in a repository
  - that was just created. -}
 headExists :: Repo -> IO Bool
diff --git a/Git/Remote.hs b/Git/Remote.hs
index dfb6a721c..9d969c416 100644
--- a/Git/Remote.hs
+++ b/Git/Remote.hs
@@ -11,6 +11,7 @@ module Git.Remote where
 
 import Common
 import Git
+import Git.Types
 import qualified Git.Command
 import qualified Git.BuildVersion
 
@@ -21,8 +22,6 @@ import Network.URI
 import Git.FilePath
 #endif
 
-type RemoteName = String
-
 {- Construct a legal git remote name out of an arbitrary input string.
  -
  - There seems to be no formal definition of this in the git source,
@@ -62,6 +61,10 @@ remoteLocationIsUrl :: RemoteLocation -> Bool
 remoteLocationIsUrl (RemoteUrl _) = True
 remoteLocationIsUrl _ = False
 
+remoteLocationIsSshUrl :: RemoteLocation -> Bool
+remoteLocationIsSshUrl (RemoteUrl u) = "ssh://" `isPrefixOf` u
+remoteLocationIsSshUrl _ = False
+
 {- Determines if a given remote location is an url, or a local
  - path. Takes the repository's insteadOf configuration into account. -}
 parseRemoteLocation :: String -> Repo -> RemoteLocation
diff --git a/Git/Repair.hs b/Git/Repair.hs
index fb877bfb7..2fe9f3896 100644
--- a/Git/Repair.hs
+++ b/Git/Repair.hs
@@ -8,12 +8,14 @@
 module Git.Repair (
 	runRepair,
 	runRepairOf,
+	successfulRepair,
 	cleanCorruptObjects,
 	retrieveMissingObjects,
 	resetLocalBranches,
 	removeTrackingBranches,
-	rewriteIndex,
 	checkIndex,
+	missingIndex,
+	nukeIndex,
 	emptyGoodCommits,
 ) where
 
@@ -34,71 +36,38 @@ import qualified Git.UpdateIndex as UpdateIndex
 import qualified Git.Branch as Branch
 import Utility.Tmp
 import Utility.Rsync
+import Utility.FileMode
 
 import qualified Data.Set as S
 import qualified Data.ByteString.Lazy as L
 import Data.Tuple.Utils
 
-{- Given a set of bad objects found by git fsck, removes all
- - corrupt objects, and returns a list of missing objects,
- - which need to be found elsewhere to finish recovery.
- -
- - Since git fsck may crash on corrupt objects, and so not
- - report the full set of corrupt or missing objects,
- - this removes corrupt objects, and re-runs fsck, until it
- - stabalizes.
- -
- - To remove corrupt objects, unpack all packs, and remove the packs
- - (to handle corrupt packs), and remove loose object files.
+{- Given a set of bad objects found by git fsck, which may not
+ - be complete, finds and removes all corrupt objects, and
+ - returns a list of missing objects, which need to be
+ - found elsewhere to finish recovery.
  -}
-cleanCorruptObjects :: FsckResults -> Repo -> IO MissingObjects
-cleanCorruptObjects mmissing r = check mmissing
-  where
-	check Nothing = do
-		putStrLn "git fsck found a problem but no specific broken objects. Perhaps a corrupt pack file?"
-		ifM (explodePacks r)
-			( retry S.empty
-			, return S.empty
-			)
-	check (Just bad)
-		| S.null bad = return S.empty
-		| otherwise = do
-			putStrLn $ unwords 
-				[ "git fsck found"
-				, show (S.size bad)
-				, "broken objects."
-				]
-			exploded <- explodePacks r
-			removed <- removeLoose r bad
-			if exploded || removed
-				then retry bad
-				else return bad
-	retry oldbad = do
-		putStrLn "Re-running git fsck to see if it finds more problems."
-		v <- findBroken False r
-		case v of
-			Nothing -> error $ unwords
-				[ "git fsck found a problem, which was not corrected after removing"
-				, show (S.size oldbad)
-				, "corrupt objects."
-				]
-			Just newbad -> do
-				removed <- removeLoose r newbad
-				let s = S.union oldbad newbad
-				if not removed || s == oldbad
-					then return s
-					else retry s
+cleanCorruptObjects :: FsckResults -> Repo -> IO (Maybe MissingObjects)
+cleanCorruptObjects fsckresults r = do
+	void $ explodePacks r
+	objs <- listLooseObjectShas r
+	bad <- findMissing objs r
+	void $ removeLoose r $ S.union bad (fromMaybe S.empty fsckresults)
+	-- Rather than returning the loose objects that were removed, re-run
+	-- fsck. Other missing objects may have been in the packs,
+	-- and this way fsck will find them.
+	findBroken False r
 
 removeLoose :: Repo -> MissingObjects -> IO Bool
 removeLoose r s = do
-	let fs = map (looseObjectFile r) (S.toList s)
-	count <- length <$> filterM doesFileExist fs
-	if (count > 0)
+	fs <- filterM doesFileExist (map (looseObjectFile r) (S.toList s))
+	let count = length fs
+	if count > 0
 		then do
 			putStrLn $ unwords
-				[ "removing"
+				[ "Removing"
 				, show count
-				, "corrupt loose objects"
+				, "corrupt loose objects."
 				]
 			mapM_ nukeFile fs
 			return True
@@ -114,57 +83,62 @@ explodePacks r = do
 			mapM_ go packs
 			return True
   where
-	go packfile = do
+	go packfile = withTmpFileIn (localGitDir r) "pack" $ \tmp _ -> do
+		moveFile packfile tmp
+		nukeFile $ packIdxFile packfile
+		allowRead tmp
 		-- May fail, if pack file is corrupt.
 		void $ tryIO $
-			pipeWrite [Param "unpack-objects"] r $ \h ->
-				L.hPut h =<< L.readFile packfile
-		nukeFile packfile
-		nukeFile $ packIdxFile packfile
+			pipeWrite [Param "unpack-objects", Param "-r"] r $ \h ->
+				L.hPut h =<< L.readFile tmp
 
 {- Try to retrieve a set of missing objects, from the remotes of a
  - repository. Returns any that could not be retreived.
- - 
+ -
  - If another clone of the repository exists locally, which might not be a
  - remote of the repo being repaired, its path can be passed as a reference
  - repository.
+ 
+ - Can also be run with Nothing, if it's not known which objects are
+ - missing, just that some are. (Ie, fsck failed badly.)
  -}
-retrieveMissingObjects :: MissingObjects -> Maybe FilePath -> Repo -> IO MissingObjects
+retrieveMissingObjects :: Maybe MissingObjects -> Maybe FilePath -> Repo -> IO (Maybe MissingObjects)
 retrieveMissingObjects missing referencerepo r
-	| S.null missing = return missing
+	| missing == Just S.empty = return $ Just S.empty
 	| otherwise = withTmpDir "tmprepo" $ \tmpdir -> do
 		unlessM (boolSystem "git" [Params "init", File tmpdir]) $
 			error $ "failed to create temp repository in " ++ tmpdir
 		tmpr <- Config.read =<< Construct.fromAbsPath tmpdir
 		stillmissing <- pullremotes tmpr (remotes r) fetchrefstags missing
-		if S.null stillmissing
-			then return stillmissing
+		if stillmissing == Just S.empty
+			then return $ Just S.empty
 			else pullremotes tmpr (remotes r) fetchallrefs stillmissing
   where
 	pullremotes tmpr [] fetchrefs stillmissing = case referencerepo of
 		Nothing -> return stillmissing
 		Just p -> ifM (fetchfrom p fetchrefs tmpr)
 			( do
+				void $ explodePacks tmpr
 				void $ copyObjects tmpr r
-				findMissing (S.toList stillmissing) r
+				case stillmissing of
+					Nothing -> return $ Just S.empty
+					Just s -> Just <$> findMissing (S.toList s) r
 			, return stillmissing
 			)
-	pullremotes tmpr (rmt:rmts) fetchrefs s
-		| S.null s = return s
+	pullremotes tmpr (rmt:rmts) fetchrefs ms
+		| ms == Just S.empty = return $ Just S.empty
 		| otherwise = do
-			putStrLn $ "Trying to recover missing objects from remote " ++ repoDescribe rmt
+			putStrLn $ "Trying to recover missing objects from remote " ++ repoDescribe rmt ++ "."
 			ifM (fetchfrom (repoLocation rmt) fetchrefs tmpr)
 				( do
+					void $ explodePacks tmpr
 					void $ copyObjects tmpr r
-					stillmissing <- findMissing (S.toList s) r
-					pullremotes tmpr rmts fetchrefs stillmissing
-				, do
-					putStrLn $ unwords
-						[ "failed to fetch from remote"
-						, repoDescribe rmt
-						, "(will continue without it, but making this remote available may improve recovery)"
-						]
-					pullremotes tmpr rmts fetchrefs s
+					case ms of
+						Nothing -> pullremotes tmpr rmts fetchrefs ms
+						Just s -> do
+							stillmissing <- findMissing (S.toList s) r
+							pullremotes tmpr rmts fetchrefs (Just stillmissing)
+				, pullremotes tmpr rmts fetchrefs ms
 				)
 	fetchfrom fetchurl ps = runBool $
 		[ Param "fetch"
@@ -178,7 +152,7 @@ retrieveMissingObjects missing referencerepo r
 	fetchallrefs = [ Param "+*:*" ]
 
 {- Copies all objects from the src repository to the dest repository.
- - This is done using rsync, so it copies all missing object, and all
+ - This is done using rsync, so it copies all missing objects, and all
  - objects they rely on. -}
 copyObjects :: Repo -> Repo -> IO Bool
 copyObjects srcr destr = rsync
@@ -237,51 +211,44 @@ removeTrackingBranches missing goodcommits r =
 {- Gets all refs, including ones that are corrupt.
  - git show-ref does not output refs to commits that are directly
  - corrupted, so it is not used.
+ -
+ - Relies on packed refs being exploded before it's called.
  -}
 getAllRefs :: Repo -> IO [Ref]
-getAllRefs r = do
-	packedrs <- mapMaybe parsePacked . lines
-		<$> catchDefaultIO "" (readFile $ packedRefsFile r)
-	loosers <- map toref <$> dirContentsRecursive refdir
-	return $ packedrs ++ loosers
+getAllRefs r = map toref <$> dirContentsRecursive refdir
   where
   	refdir = localGitDir r </> "refs"
 	toref = Ref . relPathDirToFile (localGitDir r)
 
+explodePackedRefsFile :: Repo -> IO ()
+explodePackedRefsFile r = do
+	let f = packedRefsFile r
+	whenM (doesFileExist f) $ do
+		rs <- mapMaybe parsePacked . lines
+			<$> catchDefaultIO "" (safeReadFile f)
+		forM_ rs makeref
+		nukeFile f
+  where
+	makeref (sha, ref) = do
+		let dest = localGitDir r ++ show ref
+		createDirectoryIfMissing True (parentDir dest)
+		unlessM (doesFileExist dest) $
+			writeFile dest (show sha)
+
 packedRefsFile :: Repo -> FilePath
 packedRefsFile r = localGitDir r </> "packed-refs"
 
-parsePacked :: String -> Maybe Ref
+parsePacked :: String -> Maybe (Sha, Ref)
 parsePacked l = case words l of
 	(sha:ref:[])
-		| isJust (extractSha sha) -> Just $ Ref ref
+		| isJust (extractSha sha) && Ref.legal True ref ->
+			Just (Ref sha, Ref ref)
 	_ -> Nothing
 
 {- git-branch -d cannot be used to remove a branch that is directly
- - pointing to a corrupt commit. However, it's tried first. -}
+ - pointing to a corrupt commit. -}
 nukeBranchRef :: Branch -> Repo -> IO ()
-nukeBranchRef b r = void $ usegit <||> byhand
-  where
-	usegit = runBool
-		[ Param "branch"
-		, Params "-r -d"
-		, Param $ show $ Ref.base b
-		] r
-	byhand = do
-		nukeFile $ localGitDir r </> show b
-		whenM (doesFileExist packedrefs) $
-			withTmpFile "packed-refs" $ \tmp h -> do
-				ls <- lines <$> readFile packedrefs
-				hPutStr h $ unlines $
-					filter (not . skiprefline) ls
-				hClose h
-				renameFile tmp packedrefs
-		return True
-	skiprefline l = case parsePacked l of
-		Just packedref
-			| packedref == b -> True
-		_ -> False
-	packedrefs = packedRefsFile r
+nukeBranchRef b r = nukeFile $ localGitDir r </> show b
 
 {- Finds the most recent commit to a branch that does not need any
  - of the missing objects. If the input branch is good as-is, returns it.
@@ -368,7 +335,9 @@ verifyTree missing treesha r
 			-- as long as ls-tree succeeded, we're good
 			else cleanup
 
-{- Checks that the index file only refers to objects that are not missing. -}
+{- Checks that the index file only refers to objects that are not missing,
+ - and is not itself corrupt. Note that a missing index file is not
+ - considered a problem (repo may be new). -}
 checkIndex :: MissingObjects -> Repo -> IO Bool
 checkIndex missing r = do
 	(bad, _good, cleanup) <- partitionIndex missing r
@@ -378,6 +347,9 @@ checkIndex missing r = do
 			void cleanup
 			return False
 
+missingIndex :: Repo -> IO Bool
+missingIndex r = not <$> doesFileExist (localGitDir r </> "index")
+
 partitionIndex :: MissingObjects -> Repo -> IO ([LsFiles.StagedDetails], [LsFiles.StagedDetails], IO Bool)
 partitionIndex missing r = do
 	(indexcontents, cleanup) <- LsFiles.stagedDetails [repoPath r] r
@@ -396,7 +368,7 @@ rewriteIndex missing r
 	| otherwise = do
 		(bad, good, cleanup) <- partitionIndex missing r
 		unless (null bad) $ do
-			nukeFile (localGitDir r </> "index")
+			nukeIndex r
 			UpdateIndex.streamUpdateIndex r
 				=<< (catMaybes <$> mapM reinject good)
 		void cleanup
@@ -408,6 +380,9 @@ rewriteIndex missing r
 			UpdateIndex.stageFile sha blobtype file r
 	reinject _ = return Nothing
 
+nukeIndex :: Repo -> IO ()
+nukeIndex r = nukeFile (localGitDir r </> "index")
+
 newtype GoodCommits = GoodCommits (S.Set Sha)
 
 emptyGoodCommits :: GoodCommits
@@ -432,39 +407,88 @@ displayList items header
 		| numitems > 10 = take 10 items ++ ["(and " ++ show (numitems - 10) ++ " more)"]
 		| otherwise = items
 
+{- Fix problems that would prevent repair from working at all
+ -
+ - A missing or corrupt .git/HEAD makes git not treat the repository as a
+ - git repo. If there is a git repo in a parent directory, it may move up
+ - the tree and use that one instead. So, cannot use `git show-ref HEAD` to
+ - test it.
+ -
+ - Explode the packed refs file, to simplify dealing with refs, and because
+ - fsck can complain about bad refs in it.
+ -}
+preRepair :: Repo -> IO ()
+preRepair g = do
+	unlessM (validhead <$> catchDefaultIO "" (safeReadFile headfile)) $ do
+		nukeFile headfile
+		writeFile headfile "ref: refs/heads/master"
+	explodePackedRefsFile g
+  where
+	headfile = localGitDir g </> "HEAD"
+	validhead s = "ref: refs/" `isPrefixOf` s || isJust (extractSha s)
+
 {- Put it all together. -}
 runRepair :: Bool -> Repo -> IO (Bool, MissingObjects, [Branch])
 runRepair forced g = do
+	preRepair g
 	putStrLn "Running git fsck ..."
 	fsckresult <- findBroken False g
 	if foundBroken fsckresult
-		then runRepairOf fsckresult forced Nothing g
+		then runRepair' fsckresult forced Nothing g
 		else do
 			putStrLn "No problems found."
 			return (True, S.empty, [])
 
 runRepairOf :: FsckResults -> Bool -> Maybe FilePath -> Repo -> IO (Bool, MissingObjects, [Branch])
 runRepairOf fsckresult forced referencerepo g = do
+	preRepair g
+	runRepair' fsckresult forced referencerepo g
+
+runRepair' :: FsckResults -> Bool -> Maybe FilePath -> Repo -> IO (Bool, MissingObjects, [Branch])
+runRepair' fsckresult forced referencerepo g = do
 	missing <- cleanCorruptObjects fsckresult g
 	stillmissing <- retrieveMissingObjects missing referencerepo g
-	if S.null stillmissing
-		then successfulfinish stillmissing []
-		else do
-			putStrLn $ unwords
-				[ show (S.size stillmissing)
-				, "missing objects could not be recovered!"
-				]
-			if forced
-				then continuerepairs stillmissing
-				else unsuccessfulfinish stillmissing
+	case stillmissing of
+		Just s
+			| S.null s -> if repoIsLocalBare g
+				then successfulfinish S.empty []
+				else ifM (checkIndex S.empty g)
+					( successfulfinish s []
+					, do
+						putStrLn "No missing objects found, but the index file is corrupt!"
+						if forced
+							then corruptedindex
+							else needforce S.empty
+					)
+			| otherwise -> if forced
+				then ifM (checkIndex s g)
+					( continuerepairs s
+					, corruptedindex
+					)
+				else do
+					putStrLn $ unwords
+						[ show (S.size s)
+						, "missing objects could not be recovered!"
+						]
+					unsuccessfulfinish s
+		Nothing
+			| forced -> ifM (pure (repoIsLocalBare g) <||> checkIndex S.empty g)
+				( do
+					missing' <- cleanCorruptObjects Nothing g
+					case missing' of
+						Nothing -> return (False, S.empty, [])
+						Just stillmissing' -> continuerepairs stillmissing'
+				, corruptedindex
+				)
+			| otherwise -> unsuccessfulfinish S.empty
   where
 	continuerepairs stillmissing = do
 		(remotebranches, goodcommits) <- removeTrackingBranches stillmissing emptyGoodCommits g
 		unless (null remotebranches) $
 			putStrLn $ unwords
-				[ "removed"
+				[ "Removed"
 				, show (length remotebranches)
-				, "remote tracking branches that referred to missing objects"
+				, "remote tracking branches that referred to missing objects."
 				]
 		(resetbranches, deletedbranches, _) <- resetLocalBranches stillmissing goodcommits g
 		displayList (map show resetbranches)
@@ -491,17 +515,37 @@ runRepairOf fsckresult forced referencerepo g = do
 				putStrLn "Successfully recovered repository!"
 				putStrLn "Please carefully check that the changes mentioned above are ok.."
 				return (True, stillmissing, modifiedbranches)
+	
+	corruptedindex = do
+		nukeIndex g
+		-- The corrupted index can prevent fsck from finding other
+		-- problems, so re-run repair.
+		fsckresult' <- findBroken False g
+		result <- runRepairOf fsckresult' forced referencerepo g
+		putStrLn "Removed the corrupted index file. You should look at what files are present in your working tree and git add them back to the index when appropriate."
+		return result
+
 	successfulfinish stillmissing modifiedbranches = do
 		mapM_ putStrLn
 			[ "Successfully recovered repository!"
-			, "You should run \"git fsck\" to make sure, but it looks like"
-			, "everything was recovered ok."
+			, "You should run \"git fsck\" to make sure, but it looks like everything was recovered ok."
 			]
 		return (True, stillmissing, modifiedbranches)
 	unsuccessfulfinish stillmissing = do
 		if repoIsLocalBare g
 			then do
-				putStrLn "If you have a clone of this bare repository, you should add it as a remote of this repository, and re-run git-recover-repository."
-				putStrLn "If there are no clones of this repository, you can instead run git-recover-repository with the --force parameter to force recovery to a possibly usable state."
-			else putStrLn "To force a recovery to a usable state, run this command again with the --force parameter."
+				putStrLn "If you have a clone of this bare repository, you should add it as a remote of this repository, and retry."
+				putStrLn "If there are no clones of this repository, you can instead retry with the --force parameter to force recovery to a possibly usable state."
+				return (False, stillmissing, [])
+			else needforce stillmissing
+	needforce stillmissing = do
+		putStrLn "To force a recovery to a usable state, retry with the --force parameter."
 		return (False, stillmissing, [])
+
+successfulRepair :: (Bool, MissingObjects, [Branch]) -> Bool
+successfulRepair = fst3
+
+safeReadFile :: FilePath -> IO String
+safeReadFile f = do
+	allowRead f
+	readFileStrictAnyEncoding f
diff --git a/Git/Types.hs b/Git/Types.hs
index abfb99f9f..e63e93077 100644
--- a/Git/Types.hs
+++ b/Git/Types.hs
@@ -10,6 +10,7 @@ module Git.Types where
 import Network.URI
 import qualified Data.Map as M
 import System.Posix.Types
+import Utility.SafeCommand
 
 {- Support repositories on local disk, and repositories accessed via an URL.
  -
@@ -35,11 +36,15 @@ data Repo = Repo
 	, fullconfig :: M.Map String [String]
 	, remotes :: [Repo]
 	-- remoteName holds the name used for this repo in remotes
-	, remoteName :: Maybe String
+	, remoteName :: Maybe RemoteName
 	-- alternate environment to use when running git commands
 	, gitEnv :: Maybe [(String, String)]
+	-- global options to pass to git when running git commands
+	, gitGlobalOpts :: [CommandParam]
 	} deriving (Show, Eq)
 
+type RemoteName = String
+
 {- A git ref. Can be a sha1, or a branch or tag name. -}
 newtype Ref = Ref String
 	deriving (Eq, Ord)
diff --git a/Git/Url.hs b/Git/Url.hs
index 7befc4669..d383a6aca 100644
--- a/Git/Url.hs
+++ b/Git/Url.hs
@@ -37,32 +37,33 @@ uriRegName' a = fixup $ uriRegName a
 	fixup x = x
 
 {- Hostname of an URL repo. -}
-host :: Repo -> String
+host :: Repo -> Maybe String
 host = authpart uriRegName'
 
 {- Port of an URL repo, if it has a nonstandard one. -}
 port :: Repo -> Maybe Integer
 port r = 
 	case authpart uriPort r of
-		":" -> Nothing
-		(':':p) -> readish p
-		_ -> Nothing
+		Nothing -> Nothing
+		Just ":" -> Nothing
+		Just (':':p) -> readish p
+		Just _ -> Nothing
 
 {- Hostname of an URL repo, including any username (ie, "user@host") -}
-hostuser :: Repo -> String
-hostuser r = authpart uriUserInfo r ++ authpart uriRegName' r
+hostuser :: Repo -> Maybe String
+hostuser r = (++)
+	<$> authpart uriUserInfo r
+	<*> authpart uriRegName' r
 
 {- The full authority portion an URL repo. (ie, "user@host:port") -}
-authority :: Repo -> String
+authority :: Repo -> Maybe String
 authority = authpart assemble
   where
 	assemble a = uriUserInfo a ++ uriRegName' a ++ uriPort a
 
 {- Applies a function to extract part of the uriAuthority of an URL repo. -}
-authpart :: (URIAuth -> a) -> Repo -> a
-authpart a Repo { location = Url u } = a auth
-  where
-	auth = fromMaybe (error $ "bad url " ++ show u) (uriAuthority u)
+authpart :: (URIAuth -> a) -> Repo -> Maybe a
+authpart a Repo { location = Url u } = a <$> uriAuthority u
 authpart _ repo = notUrl repo
 
 notUrl :: Repo -> a
diff --git a/GitAnnex.hs b/GitAnnex.hs
index b73cd9416..61d8b918a 100644
--- a/GitAnnex.hs
+++ b/GitAnnex.hs
@@ -5,7 +5,7 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
+{-# LANGUAGE CPP, OverloadedStrings #-}
 
 module GitAnnex where
 
@@ -46,6 +46,7 @@ import qualified Command.Whereis
 import qualified Command.List
 import qualified Command.Log
 import qualified Command.Merge
+import qualified Command.Info
 import qualified Command.Status
 import qualified Command.Migrate
 import qualified Command.Uninit
@@ -87,6 +88,9 @@ import qualified Command.XMPPGit
 import qualified Command.Test
 import qualified Command.FuzzTest
 #endif
+#ifdef WITH_EKG
+import System.Remote.Monitoring
+#endif
 
 cmds :: [Command]
 cmds = concat
@@ -140,6 +144,7 @@ cmds = concat
 	, Command.List.def
 	, Command.Log.def
 	, Command.Merge.def
+	, Command.Info.def
 	, Command.Status.def
 	, Command.Migrate.def
 	, Command.Map.def
@@ -169,4 +174,8 @@ header :: String
 header = "git-annex command [option ...]"
 
 run :: [String] -> IO ()
-run args = dispatch True args cmds options [] header Git.CurrentRepo.get
+run args = do
+#ifdef WITH_EKG
+	_ <- forkServer "localhost" 4242
+#endif
+	dispatch True args cmds options [] header Git.CurrentRepo.get
diff --git a/GitAnnex/Options.hs b/GitAnnex/Options.hs
index 7f4cb60c2..88fad948a 100644
--- a/GitAnnex/Options.hs
+++ b/GitAnnex/Options.hs
@@ -11,6 +11,7 @@ import System.Console.GetOpt
 
 import Common.Annex
 import qualified Git.Config
+import Git.Types
 import Command
 import Types.TrustLevel
 import qualified Annex
@@ -59,12 +60,14 @@ options = Option.common ++
 		"Trust Amazon Glacier inventory"
 	] ++ Option.matcher
   where
+	trustArg t = ReqArg (Remote.forceTrust t) paramRemote
 	setnumcopies v = maybe noop
 		(\n -> Annex.changeState $ \s -> s { Annex.forcenumcopies = Just n })
 		(readish v)
 	setuseragent v = Annex.changeState $ \s -> s { Annex.useragent = Just v }
-	setgitconfig v = Annex.changeGitRepo =<< inRepo (Git.Config.store v)
-	trustArg t = ReqArg (Remote.forceTrust t) paramRemote
+	setgitconfig v = inRepo (Git.Config.store v)
+		>>= pure . (\r -> r { gitGlobalOpts = gitGlobalOpts r ++ [Param "-c", Param v] })
+		>>= Annex.changeGitRepo
 
 keyOptions :: [Option]
 keyOptions = 
diff --git a/Init.hs b/Init.hs
index 7e7e5041d..ad1803995 100644
--- a/Init.hs
+++ b/Init.hs
@@ -12,11 +12,10 @@ module Init (
 	isInitialized,
 	initialize,
 	uninitialize,
-	probeCrippledFileSystem
+	probeCrippledFileSystem,
 ) where
 
 import Common.Annex
-import Utility.Tmp
 import Utility.Network
 import qualified Annex
 import qualified Git
@@ -26,16 +25,18 @@ import qualified Annex.Branch
 import Logs.UUID
 import Annex.Version
 import Annex.UUID
-import Utility.Shell
 import Config
 import Annex.Direct
 import Annex.Content.Direct
 import Annex.Environment
+import Annex.Perms
 import Backend
 #ifndef mingw32_HOST_OS
 import Utility.UserInfo
 import Utility.FileMode
 #endif
+import Annex.Hook
+import Upgrade
 
 genDescription :: Maybe String -> Annex String
 genDescription (Just d) = return d
@@ -53,10 +54,19 @@ genDescription Nothing = do
 initialize :: Maybe String -> Annex ()
 initialize mdescription = do
 	prepUUID
-	setVersion defaultVersion
-	checkCrippledFileSystem
 	checkFifoSupport
-	gitPreCommitHookWrite
+	checkCrippledFileSystem
+	unlessM isBare $
+		hookWrite preCommitHook
+	ifM (crippledFileSystem <&&> not <$> isBare)
+		( do
+			enableDirectMode
+			setDirect True
+			setVersion directModeVersion
+		, do
+			setVersion defaultVersion
+			setDirect False
+		)
 	createInodeSentinalFile
 	u <- getUUID
 	{- This will make the first commit to git, so ensure git is set up
@@ -67,16 +77,19 @@ initialize mdescription = do
 
 uninitialize :: Annex ()
 uninitialize = do
-	gitPreCommitHookUnWrite
+	hookUnWrite preCommitHook
 	removeRepoUUID
 	removeVersion
 
 {- Will automatically initialize if there is already a git-annex
  - branch from somewhere. Otherwise, require a manual init
  - to avoid git-annex accidentially being run in git
- - repos that did not intend to use it. -}
+ - repos that did not intend to use it.
+ -
+ - Checks repository version and handles upgrades too.
+ -}
 ensureInitialized :: Annex ()
-ensureInitialized = getVersion >>= maybe needsinit checkVersion
+ensureInitialized = getVersion >>= maybe needsinit checkUpgrade
   where
 	needsinit = ifM Annex.Branch.hasSibling
 			( initialize Nothing
@@ -87,45 +100,8 @@ ensureInitialized = getVersion >>= maybe needsinit checkVersion
 isInitialized :: Annex Bool
 isInitialized = maybe Annex.Branch.hasSibling (const $ return True) =<< getVersion
 
-{- set up a git pre-commit hook, if one is not already present -}
-gitPreCommitHookWrite :: Annex ()
-gitPreCommitHookWrite = unlessBare $ do
-	hook <- preCommitHook
-	ifM (liftIO $ doesFileExist hook)
-		( do
-			content <- liftIO $ readFile hook
-			when (content /= preCommitScript) $
-				warning $ "pre-commit hook (" ++ hook ++ ") already exists, not configuring"
-		, unlessM crippledFileSystem $
-			liftIO $ do
-				viaTmp writeFile hook preCommitScript
-				p <- getPermissions hook
-				setPermissions hook $ p {executable = True}
-		)
-
-gitPreCommitHookUnWrite :: Annex ()
-gitPreCommitHookUnWrite = unlessBare $ do
-	hook <- preCommitHook
-	whenM (liftIO $ doesFileExist hook) $
-		ifM (liftIO $ (==) preCommitScript <$> readFile hook)
-			( liftIO $ removeFile hook
-			, warning $ "pre-commit hook (" ++ hook ++ 
-				") contents modified; not deleting." ++
-				" Edit it to remove call to git annex."
-			)
-
-unlessBare :: Annex () -> Annex ()
-unlessBare = unlessM $ fromRepo Git.repoIsLocalBare
-
-preCommitHook :: Annex FilePath
-preCommitHook = (</>) <$> fromRepo Git.localGitDir <*> pure "hooks/pre-commit"
-
-preCommitScript :: String
-preCommitScript = unlines
-	[ shebang_local
-	, "# automatically configured by git-annex"
-	, "git annex pre-commit ."
-	]
+isBare :: Annex Bool
+isBare = fromRepo Git.repoIsLocalBare
 
 {- A crippled filesystem is one that does not allow making symlinks,
  - or removing write access from files. -}
@@ -136,9 +112,8 @@ probeCrippledFileSystem = do
 #else
 	tmp <- fromRepo gitAnnexTmpDir
 	let f = tmp </> "gaprobe"
-	liftIO $ do
-		createDirectoryIfMissing True tmp
-		writeFile f ""
+	createAnnexDirectory tmp
+	liftIO $ writeFile f ""
 	uncrippled <- liftIO $ probe f
 	liftIO $ removeFile f
 	return $ not uncrippled
@@ -158,25 +133,15 @@ checkCrippledFileSystem = whenM probeCrippledFileSystem $ do
 	warning "Detected a crippled filesystem."
 	setCrippledFileSystem True
 
-	{- Normally git disables core.symlinks itself when the filesystem does
- 	 - not support them, but in Cygwin, git does support symlinks, while
- 	 - git-annex, not linking with Cygwin, does not. -}
+	{- Normally git disables core.symlinks itself when the
+	 - filesystem does not support them, but in Cygwin, git
+	 - does support symlinks, while git-annex, not linking
+	 - with Cygwin, does not. -}
 	whenM (coreSymlinks <$> Annex.getGitConfig) $ do
 		warning "Disabling core.symlinks."
 		setConfig (ConfigKey "core.symlinks")
 			(Git.Config.boolConfig False)
 
-	unlessBare $ do
-		unlessM isDirect $ do
-			warning "Enabling direct mode."
-			top <- fromRepo Git.repoPath
-			(l, clean) <- inRepo $ Git.LsFiles.inRepo [top]
-			forM_ l $ \f ->
-				maybe noop (`toDirect` f) =<< isAnnexLink f
-			void $ liftIO clean
-			setDirect True
-		setVersion directModeVersion
-
 probeFifoSupport :: Annex Bool
 probeFifoSupport = do
 #ifdef mingw32_HOST_OS
@@ -184,8 +149,8 @@ probeFifoSupport = do
 #else
 	tmp <- fromRepo gitAnnexTmpDir
 	let f = tmp </> "gaprobe"
+	createAnnexDirectory tmp
 	liftIO $ do
-		createDirectoryIfMissing True tmp
 		nukeFile f
 		ms <- tryIO $ do
 			createNamedPipe f ownerReadMode
@@ -199,3 +164,12 @@ checkFifoSupport = unlessM probeFifoSupport $ do
 	warning "Detected a filesystem without fifo support."
 	warning "Disabling ssh connection caching."
 	setConfig (annexConfig "sshcaching") (Git.Config.boolConfig False)
+
+enableDirectMode :: Annex ()
+enableDirectMode = unlessM isDirect $ do
+	warning "Enabling direct mode."
+	top <- fromRepo Git.repoPath
+	(l, clean) <- inRepo $ Git.LsFiles.inRepo [top]
+	forM_ l $ \f ->
+		maybe noop (`toDirect` f) =<< isAnnexLink f
+	void $ liftIO clean
diff --git a/Logs/UUID.hs b/Logs/UUID.hs
index ef1074e78..154f86d51 100644
--- a/Logs/UUID.hs
+++ b/Logs/UUID.hs
@@ -56,7 +56,7 @@ fixBadUUID = M.fromList . map fixup . M.toList
 		| otherwise = (k, v)
 	  where
 		kuuid = fromUUID k
-		isbad = not (isuuid kuuid) && isuuid lastword
+		isbad = not (isuuid kuuid) && not (null ws) && isuuid lastword
 		ws = words $ value v
 		lastword = Prelude.last ws
 		fixeduuid = toUUID lastword
diff --git a/Logs/UUIDBased.hs b/Logs/UUIDBased.hs
index c1901eef7..10b3bf55d 100644
--- a/Logs/UUIDBased.hs
+++ b/Logs/UUIDBased.hs
@@ -63,6 +63,11 @@ parseLogWithUUID :: (UUID -> String -> Maybe a) -> String -> Log a
 parseLogWithUUID parser = M.fromListWith best . mapMaybe parse . lines
   where
 	parse line
+		-- This is a workaround for a bug that caused
+		-- NoUUID items to be stored in the log.
+		-- It can be removed at any time; is just here to clean
+		-- up logs where that happened temporarily.
+		| " " `isPrefixOf` line = Nothing
 		| null ws = Nothing
 		| otherwise = parser u (unwords info) >>= makepair
 	  where
diff --git a/Makefile b/Makefile
index 0f8fdd849..92c5f6dcc 100644
--- a/Makefile
+++ b/Makefile
@@ -30,12 +30,8 @@ git-annex-shell.1: doc/git-annex-shell.mdwn
 # These are not built normally.
 git-union-merge.1: doc/git-union-merge.mdwn
 	./Build/mdwn2man git-union-merge 1 doc/git-union-merge.mdwn > git-union-merge.1
-git-recover-repository.1: doc/git-recover-repository.mdwn
-	./Build/mdwn2man git-recover-repository 1 doc/git-recover-repository.mdwn > git-recover-repository.1
 git-union-merge:
 	$(GHC) --make -threaded $@
-git-recover-repository:
-	$(GHC) --make -threaded $@
 
 install-mans: $(mans)
 	install -d $(DESTDIR)$(PREFIX)/share/man/man1
@@ -81,10 +77,10 @@ clean:
 	rm -rf tmp dist git-annex $(mans) configure  *.tix .hpc \
 		doc/.ikiwiki html dist tags Build/SysConfig.hs build-stamp \
 		Setup Build/InstallDesktopFile Build/EvilSplicer \
-		Build/Standalone Build/OSXMkLibs \
-		git-union-merge git-recover-repository
-	find -name \*.o -exec rm {} \;
-	find -name \*.hi -exec rm {} \;
+		Build/Standalone Build/OSXMkLibs Build/DistributionUpdate \
+		git-union-merge
+	find . -name \*.o -exec rm {} \;
+	find . -name \*.hi -exec rm {} \;
 
 Build/InstallDesktopFile: Build/InstallDesktopFile.hs
 	$(GHC) --make $@
@@ -137,6 +133,8 @@ linuxstandalone: Build/Standalone
 	sort "$(LINUXSTANDALONE_DEST)/libdirs.tmp" | uniq > "$(LINUXSTANDALONE_DEST)/libdirs"
 	rm -f "$(LINUXSTANDALONE_DEST)/libdirs.tmp"
 
+	cd tmp/git-annex.linux && find . -type f > git-annex.MANIFEST
+	cd tmp/git-annex.linux && find . -type l >> git-annex.MANIFEST
 	cd tmp && tar czf git-annex-standalone-$(shell dpkg --print-architecture).tar.gz git-annex.linux
 
 OSXAPP_DEST=tmp/build-dmg/git-annex.app
@@ -161,18 +159,18 @@ osxapp: Build/Standalone Build/OSXMkLibs
 	install -d "$(OSXAPP_BASE)/templates"
 
 	./Build/OSXMkLibs $(OSXAPP_BASE)
+	cd $(OSXAPP_DEST) && find . -type f > Contents/MacOS/git-annex.MANIFEST
+	cd $(OSXAPP_DEST) && find . -type l >> Contents/MacOS/git-annex.MANIFEST
 	rm -f tmp/git-annex.dmg
-	hdiutil create -size 640m -format UDRW -srcfolder tmp/build-dmg \
+	hdiutil create -format UDBZ -srcfolder tmp/build-dmg \
 		-volname git-annex -o tmp/git-annex.dmg
-	rm -f tmp/git-annex.dmg.bz2
-	bzip2 --fast tmp/git-annex.dmg
 
-ANDROID_FLAGS?=-f-XMPP
+ANDROID_FLAGS?=
 # Cross compile for Android.
 # Uses https://github.com/neurocyte/ghc-android
 android: Build/EvilSplicer
 	echo "Running native build, to get TH splices.."
-	if [ ! -e dist/setup/setup ]; then $(CABAL) configure -f-Production -O0 $(ANDROID_FLAGS);  fi
+	if [ ! -e dist/setup/setup ]; then $(CABAL) configure -f-Production -O0 $(ANDROID_FLAGS) -fAndroidSplice;  fi
 	mkdir -p tmp
 	if ! $(CABAL) build --ghc-options=-ddump-splices 2> tmp/dump-splices; then tail tmp/dump-splices >&2; exit 1; fi
 	echo "Setting up Android build tree.."
@@ -189,14 +187,16 @@ android: Build/EvilSplicer
 	sed -i 's/GHC-Options: \(.*\)-Wall/GHC-Options: \1-Wall -fno-warn-unused-imports /i' tmp/androidtree/git-annex.cabal
 # Cabal cannot cross compile with custom build type, so workaround.
 	sed -i 's/Build-type: Custom/Build-type: Simple/' tmp/androidtree/git-annex.cabal
-	if [ ! -e tmp/androidtree/dist/setup/setup ]; then \
-		cd tmp/androidtree && $$HOME/.ghc/android-14/arm-linux-androideabi-4.7/arm-linux-androideabi/bin/cabal configure -fAndroid $(ANDROID_FLAGS); \
+# Build just once, but link twice, for 2 different versions of Android.
+	mkdir -p tmp/androidtree/dist/build/git-annex/4.0 tmp/androidtree/dist/build/git-annex/4.3
+	if [ ! -e tmp/androidtree/dist/setup-config ]; then \
+		cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal configure -fAndroid $(ANDROID_FLAGS); \
 	fi
-	cd tmp/androidtree && $$HOME/.ghc/android-14/arm-linux-androideabi-4.7/arm-linux-androideabi/bin/cabal build
-
-adb:
-	ANDROID_FLAGS="-Production" $(MAKE) android
-	adb push tmp/androidtree/dist/build/git-annex/git-annex /data/data/ga.androidterm/bin/git-annex
+	cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal build \
+		&& mv dist/build/git-annex/git-annex dist/build/git-annex/4.0/git-annex
+	cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal build \
+		--ghc-options=-optl-z --ghc-options=-optlnocopyreloc \
+		&& mv dist/build/git-annex/git-annex dist/build/git-annex/4.3/git-annex
 
 androidapp:
 	$(MAKE) android
@@ -221,4 +221,8 @@ hdevtools:
 	hdevtools --stop-server || true
 	hdevtools check git-annex.hs -g -cpp -g -i -g -idist/build/git-annex/git-annex-tmp -g -i. -g -idist/build/autogen -g -Idist/build/autogen -g -Idist/build/git-annex/git-annex-tmp -g -IUtility -g -DWITH_TESTSUITE -g -DWITH_S3 -g -DWITH_ASSISTANT -g -DWITH_INOTIFY -g -DWITH_DBUS -g -DWITH_PAIRING -g -DWITH_XMPP -g -optP-include -g -optPdist/build/autogen/cabal_macros.h -g -odir -g dist/build/git-annex/git-annex-tmp -g -hidir -g dist/build/git-annex/git-annex-tmp -g -stubdir -g dist/build/git-annex/git-annex-tmp -g -threaded -g -Wall -g -XHaskell98 -g -XPackageImports
 
+distributionupdate:
+	ghc --make Build/DistributionUpdate
+	./Build/DistributionUpdate
+
 .PHONY: git-annex git-union-merge git-recover-repository tags build-stamp
diff --git a/Remote.hs b/Remote.hs
index 71db09ce7..e355b0975 100644
--- a/Remote.hs
+++ b/Remote.hs
@@ -24,6 +24,7 @@ module Remote (
 	remoteMap,
 	uuidDescriptions,
 	byName,
+	byNameOnly,
 	byNameWithUUID,
 	byCost,
 	prettyPrintUUIDs,
@@ -58,7 +59,7 @@ import Logs.Trust
 import Logs.Location hiding (logStatus)
 import Remote.List
 import Config
-import Git.Remote
+import Git.Types (RemoteName)
 
 {- Map from UUIDs of Remotes to a calculated value. -}
 remoteMap :: (Remote -> a) -> Annex (M.Map UUID a)
@@ -89,11 +90,12 @@ byNameWithUUID = checkuuid <=< byName
   where
   	checkuuid Nothing = return Nothing
 	checkuuid (Just r)
-		| uuid r == NoUUID = do
-			let e = "cannot determine uuid for " ++ name r
+		| uuid r == NoUUID =
 			if remoteAnnexIgnore (gitconfig r)
-				then error $ e ++ " (" ++ show (remoteConfig (repo r) "ignore") ++ " is set)"
-				else error e
+				then error $ noRemoteUUIDMsg r ++
+					" (" ++ show (remoteConfig (repo r) "ignore") ++
+					" is set)"
+				else error $ noRemoteUUIDMsg r
 		| otherwise = return $ Just r
 
 byName' :: RemoteName -> Annex (Either String Remote)
@@ -104,16 +106,27 @@ byName' n = handle . filter matching <$> remoteList
 	handle (match:_) = Right match
 	matching r = n == name r || toUUID n == uuid r
 
+{- Only matches remote name, not UUID -}
+byNameOnly :: RemoteName -> Annex (Maybe Remote)
+byNameOnly n = headMaybe . filter matching <$> remoteList
+  where
+	matching r = n == name r
+
+noRemoteUUIDMsg :: Remote -> String
+noRemoteUUIDMsg r = "cannot determine uuid for " ++ name r
+
 {- Looks up a remote by name (or by UUID, or even by description),
- - and returns its UUID. Finds even remotes that are not configured in
- - .git/config. -}
+ - and returns its UUID. Finds even repositories that are not
+ - configured in .git/config. -}
 nameToUUID :: RemoteName -> Annex UUID
 nameToUUID "." = getUUID -- special case for current repo
 nameToUUID "here" = getUUID
 nameToUUID "" = error "no remote specified"
 nameToUUID n = byName' n >>= go
   where
-	go (Right r) = return $ uuid r
+	go (Right r) = case uuid r of
+		NoUUID -> error $ noRemoteUUIDMsg r
+		u -> return u
 	go (Left e) = fromMaybe (error e) <$> bydescription
 	bydescription = do
 		m <- uuidMap
diff --git a/Remote/Directory.hs b/Remote/Directory.hs
index 16535070e..e6deee4bf 100644
--- a/Remote/Directory.hs
+++ b/Remote/Directory.hs
@@ -56,7 +56,7 @@ gen r u c gc = do
 			whereisKey = Nothing,
 			remoteFsck = Nothing,
 			repairRepo = Nothing,
-			config = M.empty,
+			config = c,
 			repo = r,
 			gitconfig = gc,
 			localpath = Just dir,
diff --git a/Remote/GCrypt.hs b/Remote/GCrypt.hs
index a421668f8..e1b6811c7 100644
--- a/Remote/GCrypt.hs
+++ b/Remote/GCrypt.hs
@@ -109,7 +109,7 @@ gen' r u c gc = do
 		, whereisKey = Nothing
 		, remoteFsck = Nothing
 		, repairRepo = Nothing
-		, config = M.empty
+		, config = c
 		, localpath = localpathCalc r
 		, repo = r
 		, gitconfig = gc { remoteGitConfig = Just $ extractGitConfig r }
diff --git a/Remote/Git.hs b/Remote/Git.hs
index ba247078b..d4e5987dc 100644
--- a/Remote/Git.hs
+++ b/Remote/Git.hs
@@ -120,7 +120,7 @@ gen r u c gc
 			, repairRepo = if Git.repoIsUrl r
 				then Nothing
 				else Just $ repairRemote r
-			, config = M.empty
+			, config = c
 			, localpath = localpathCalc r
 			, repo = r
 			, gitconfig = gc
diff --git a/Remote/Helper/Ssh.hs b/Remote/Helper/Ssh.hs
index 35655f00b..8cf9275a0 100644
--- a/Remote/Helper/Ssh.hs
+++ b/Remote/Helper/Ssh.hs
@@ -30,7 +30,7 @@ toRepo r sshcmd = do
 	g <- fromRepo id
 	let c = extractRemoteGitConfig g (Git.repoDescribe r)
 	let opts = map Param $ remoteAnnexSshOptions c
-	let host = Git.Url.hostuser r
+	let host = fromMaybe (error "bad ssh url") $ Git.Url.hostuser r
 	params <- sshCachingOptions (host, Git.Url.port r) opts
 	return $ params ++ Param host : sshcmd
 
diff --git a/Remote/Hook.hs b/Remote/Hook.hs
index fdb24d0cb..55ff78514 100644
--- a/Remote/Hook.hs
+++ b/Remote/Hook.hs
@@ -54,7 +54,7 @@ gen r u c gc = do
 			whereisKey = Nothing,
 			remoteFsck = Nothing,
 			repairRepo = Nothing,
-			config = M.empty,
+			config = c,
 			localpath = Nothing,
 			repo = r,
 			gitconfig = gc,
diff --git a/Remote/Rsync.hs b/Remote/Rsync.hs
index 6bc5fd78f..91638de98 100644
--- a/Remote/Rsync.hs
+++ b/Remote/Rsync.hs
@@ -81,7 +81,7 @@ gen r u c gc = do
 			, whereisKey = Nothing
 			, remoteFsck = Nothing
 			, repairRepo = Nothing
-			, config = M.empty
+			, config = c
 			, repo = r
 			, gitconfig = gc
 			, localpath = if islocal
diff --git a/Remote/Web.hs b/Remote/Web.hs
index 7c98dbf40..0a8df35d5 100644
--- a/Remote/Web.hs
+++ b/Remote/Web.hs
@@ -25,8 +25,6 @@ import Annex.Quvi
 import qualified Utility.Quvi as Quvi
 #endif
 
-import qualified Data.Map as M
-
 remote :: RemoteType
 remote = RemoteType {
 	typename = "web",
@@ -44,7 +42,7 @@ list = do
 	return [r]
 
 gen :: Git.Repo -> UUID -> RemoteConfig -> RemoteGitConfig -> Annex (Maybe Remote)
-gen r _ _ gc = 
+gen r _ c gc = 
 	return $ Just Remote {
 		uuid = webUUID,
 		cost = expensiveRemoteCost,
@@ -58,7 +56,7 @@ gen r _ _ gc =
 		whereisKey = Just getUrls,
 		remoteFsck = Nothing,
 		repairRepo = Nothing,
-		config = M.empty,
+		config = c,
 		gitconfig = gc,
 		localpath = Nothing,
 		repo = r,
diff --git a/Seek.hs b/Seek.hs
index 7f74f6728..b2782fc36 100644
--- a/Seek.hs
+++ b/Seek.hs
@@ -141,13 +141,15 @@ withNothing _ _ = error "This command takes no parameters."
 withKeyOptions :: (Key -> CommandStart) -> CommandSeek -> CommandSeek
 withKeyOptions keyop fallbackop params = do
 	bare <- fromRepo Git.repoIsLocalBare
-	allkeys <- Annex.getFlag "all" <||> pure bare
+	allkeys <- Annex.getFlag "all"
 	unused <- Annex.getFlag "unused"
 	auto <- Annex.getState Annex.auto
-	case    (allkeys , unused, auto ) of
+	case    (allkeys || bare , unused, auto ) of
 		(True    , False , False) -> go loggedKeys
 		(False   , True  , False) -> go unusedKeys
-		(True    , True  , _    ) -> error "Cannot use --all with --unused."
+		(True    , True  , _    )
+			| bare && not allkeys -> go unusedKeys
+			| otherwise -> error "Cannot use --all with --unused."
 		(False   , False , _    ) -> fallbackop params
 		(_       , _     , True )
 			| bare -> error "Cannot use --auto in a bare repository."
diff --git a/Test.hs b/Test.hs
index 93af17585..4c7281fce 100644
--- a/Test.hs
+++ b/Test.hs
@@ -9,12 +9,14 @@
 
 module Test where
 
-import Test.HUnit
-import Test.QuickCheck
-import Test.QuickCheck.Test
+import Test.Tasty
+import Test.Tasty.Runners
+import Test.Tasty.HUnit
+import Test.Tasty.QuickCheck
 
 import System.PosixCompat.Files
 import Control.Exception.Extensible
+import Data.Monoid
 import qualified Data.Map as M
 import System.IO.HVFS (SystemFS(..))
 import qualified Text.JSON
@@ -72,111 +74,101 @@ type TestEnv = M.Map String String
 
 main :: IO ()
 main = do
-	divider
-	putStrLn "First, some automated quick checks of properties ..."
-	divider
-	qcok <- all isSuccess <$> sequence quickcheck
-	divider
-	putStrLn "Now, some broader checks ..."
-	putStrLn "  (Do not be alarmed by odd output here; it's normal."
-        putStrLn "   wait for the last line to see how it went.)"
-	rs <- runhunit =<< prepare False
 #ifndef mingw32_HOST_OS
-	directrs <- runhunit =<< prepare True
+	indirectenv <- prepare False
+	directenv <- prepare True
+	let tests = testGroup "Tests"
+		[ localOption (QuickCheckTests 1000) properties
+		, unitTests directenv "(direct)"
+		, unitTests indirectenv "(indirect)"
+		]
 #else
 	-- Windows is only going to use direct mode, so don't test twice.
-	let directrs = []
+	env <- prepare False
+	let tests = testGroup "Tests"
+		[properties, unitTests env ""]
 #endif
-	divider
-	propigate (rs++directrs) qcok
-  where
-	divider = putStrLn $ replicate 70 '-'
-	runhunit env = do
-		r <- forM hunit $ \t -> do
-			divider
-			t env
-		cleanup tmpdir
-		return r
-
-propigate :: [Counts] -> Bool -> IO ()
-propigate cs qcok
-	| countsok && qcok = putStrLn "All tests ok."
-	| otherwise = do
-		unless qcok $
-			putStrLn "Quick check tests failed! This is a bug in git-annex."
-		unless countsok $ do
-			putStrLn "Some tests failed!"
+	let runner = tryIngredients [consoleTestReporter] mempty tests
+	ifM (maybe (error "tasty failed to return a runner!") id runner)
+		( exitSuccess
+		, do
 			putStrLn "  (This could be due to a bug in git-annex, or an incompatability"
 			putStrLn "   with utilities, such as git, installed on this system.)"
-		exitFailure
-  where
-	noerrors (Counts { errors = e , failures = f }) = e + f == 0
-	countsok = all noerrors cs
-
-quickcheck :: [IO Result]
-quickcheck =
-	[ check "prop_idempotent_deencode_git" Git.Filename.prop_idempotent_deencode
-	, check "prop_idempotent_deencode" Utility.Format.prop_idempotent_deencode
-	, check "prop_idempotent_fileKey" Locations.prop_idempotent_fileKey
-	, check "prop_idempotent_key_encode" Types.Key.prop_idempotent_key_encode
-	, check "prop_idempotent_key_decode" Types.Key.prop_idempotent_key_decode
-	, check "prop_idempotent_shellEscape" Utility.SafeCommand.prop_idempotent_shellEscape
-	, check "prop_idempotent_shellEscape_multiword" Utility.SafeCommand.prop_idempotent_shellEscape_multiword
-	, check "prop_logs_sane" Logs.prop_logs_sane
-	, check "prop_idempotent_configEscape" Logs.Remote.prop_idempotent_configEscape
-	, check "prop_parse_show_Config" Logs.Remote.prop_parse_show_Config
-	, check "prop_parentDir_basics" Utility.Path.prop_parentDir_basics
-	, check "prop_relPathDirToFile_basics" Utility.Path.prop_relPathDirToFile_basics
-	, check "prop_relPathDirToFile_regressionTest" Utility.Path.prop_relPathDirToFile_regressionTest
-	, check "prop_cost_sane" Config.Cost.prop_cost_sane
-	, check "prop_matcher_sane" Utility.Matcher.prop_matcher_sane
-	, check "prop_HmacSha1WithCipher_sane" Crypto.prop_HmacSha1WithCipher_sane
-	, check "prop_TimeStamp_sane" Logs.UUIDBased.prop_TimeStamp_sane
-	, check "prop_addLog_sane" Logs.UUIDBased.prop_addLog_sane
-	, check "prop_verifiable_sane" Utility.Verifiable.prop_verifiable_sane
-	, check "prop_segment_regressionTest" Utility.Misc.prop_segment_regressionTest
-	, check "prop_read_write_transferinfo" Logs.Transfer.prop_read_write_transferinfo
-	, check "prop_read_show_inodecache" Utility.InodeCache.prop_read_show_inodecache
-	, check "prop_parse_show_log" Logs.Presence.prop_parse_show_log
-	, check "prop_read_show_TrustLevel" Types.TrustLevel.prop_read_show_TrustLevel
-	, check "prop_parse_show_TrustLog" Logs.Trust.prop_parse_show_TrustLog
-	, check "prop_hashes_stable" Utility.Hash.prop_hashes_stable
-	, check "prop_schedule_roundtrips" Utility.Scheduled.prop_schedule_roundtrips
-	, check "prop_duration_roundtrips" Utility.HumanTime.prop_duration_roundtrips
+			exitFailure
+		)
+
+properties :: TestTree
+properties = testGroup "QuickCheck"
+	[ testProperty "prop_idempotent_deencode_git" Git.Filename.prop_idempotent_deencode
+	, testProperty "prop_idempotent_deencode" Utility.Format.prop_idempotent_deencode
+	, testProperty "prop_idempotent_fileKey" Locations.prop_idempotent_fileKey
+	, testProperty "prop_idempotent_key_encode" Types.Key.prop_idempotent_key_encode
+	, testProperty "prop_idempotent_key_decode" Types.Key.prop_idempotent_key_decode
+	, testProperty "prop_idempotent_shellEscape" Utility.SafeCommand.prop_idempotent_shellEscape
+	, testProperty "prop_idempotent_shellEscape_multiword" Utility.SafeCommand.prop_idempotent_shellEscape_multiword
+	, testProperty "prop_logs_sane" Logs.prop_logs_sane
+	, testProperty "prop_idempotent_configEscape" Logs.Remote.prop_idempotent_configEscape
+	, testProperty "prop_parse_show_Config" Logs.Remote.prop_parse_show_Config
+	, testProperty "prop_parentDir_basics" Utility.Path.prop_parentDir_basics
+	, testProperty "prop_relPathDirToFile_basics" Utility.Path.prop_relPathDirToFile_basics
+	, testProperty "prop_relPathDirToFile_regressionTest" Utility.Path.prop_relPathDirToFile_regressionTest
+	, testProperty "prop_cost_sane" Config.Cost.prop_cost_sane
+	, testProperty "prop_matcher_sane" Utility.Matcher.prop_matcher_sane
+	, testProperty "prop_HmacSha1WithCipher_sane" Crypto.prop_HmacSha1WithCipher_sane
+	, testProperty "prop_TimeStamp_sane" Logs.UUIDBased.prop_TimeStamp_sane
+	, testProperty "prop_addLog_sane" Logs.UUIDBased.prop_addLog_sane
+	, testProperty "prop_verifiable_sane" Utility.Verifiable.prop_verifiable_sane
+	, testProperty "prop_segment_regressionTest" Utility.Misc.prop_segment_regressionTest
+	, testProperty "prop_read_write_transferinfo" Logs.Transfer.prop_read_write_transferinfo
+	, testProperty "prop_read_show_inodecache" Utility.InodeCache.prop_read_show_inodecache
+	, testProperty "prop_parse_show_log" Logs.Presence.prop_parse_show_log
+	, testProperty "prop_read_show_TrustLevel" Types.TrustLevel.prop_read_show_TrustLevel
+	, testProperty "prop_parse_show_TrustLog" Logs.Trust.prop_parse_show_TrustLog
+	, testProperty "prop_hashes_stable" Utility.Hash.prop_hashes_stable
+	, testProperty "prop_schedule_roundtrips" Utility.Scheduled.prop_schedule_roundtrips
+	, testProperty "prop_duration_roundtrips" Utility.HumanTime.prop_duration_roundtrips
 	]
-  where
-	check desc prop = do
-		putStrLn desc
-		quickCheckResult prop
 
-hunit :: [TestEnv -> IO Counts]
-hunit =
+unitTests :: TestEnv -> String -> TestTree
+unitTests env note = testGroup ("Unit Tests " ++ note)
 	-- test order matters, later tests may rely on state from earlier
 	[ check "init" test_init
 	, check "add" test_add
+	, check "add sha1dup" test_add_sha1dup
+	, check "add subdirs" test_add_subdirs
 	, check "reinject" test_reinject
-	, check "unannex" test_unannex
-	, check "drop" test_drop
+	, check "unannex (no copy)" test_unannex_nocopy
+	, check "unannex (with copy)" test_unannex_withcopy
+	, check "drop (no remote)" test_drop_noremote
+	, check "drop (with remote)" test_drop_withremote
+	, check "drop (untrusted remote)" test_drop_untrustedremote
 	, check "get" test_get
 	, check "move" test_move
 	, check "copy" test_copy
 	, check "lock" test_lock
-	, check "edit" test_edit
+	, check "edit (no pre-commit)" test_edit
+	, check "edit (pre-commit)" test_edit_precommit
 	, check "fix" test_fix
 	, check "trust" test_trust
-	, check "fsck" test_fsck
+	, check "fsck (basics)" test_fsck_basic
+	, check "fsck (bare)" test_fsck_bare
+	, check "fsck (local untrusted)" test_fsck_localuntrusted
+	, check "fsck (remote untrusted)" test_fsck_remoteuntrusted
 	, check "migrate" test_migrate
+	, check "migrate (via gitattributes)" test_migrate_via_gitattributes
 	, check" unused" test_unused
 	, check "describe" test_describe
 	, check "find" test_find
 	, check "merge" test_merge
-	, check "status" test_status
+	, check "info" test_info
 	, check "version" test_version
 	, check "sync" test_sync
 	, check "union merge regression" test_union_merge_regression
-	, check "conflict resolution" test_conflict_resolution
+	, check "conflict resolution" test_conflict_resolution_movein_bug
+	, check "conflict_resolution (mixed directory and file)" test_mixed_conflict_resolution
 	, check "map" test_map
 	, check "uninit" test_uninit
+	, check "uninit (in git-annex branch)" test_uninit_inbranch
 	, check "upgrade" test_upgrade
 	, check "whereis" test_whereis
 	, check "hook remote" test_hook_remote
@@ -185,61 +177,74 @@ hunit =
 	, check "bup remote" test_bup_remote
 	, check "crypto" test_crypto
 	, check "preferred content" test_preferred_content
+	, check "global cleanup" test_global_cleanup
 	]
   where
-	check desc t env = do
-		putStrLn desc
-		runTestTT (t env)
+	check desc t = testCase desc (t env)
+
+test_global_cleanup :: TestEnv -> Assertion
+test_global_cleanup _env = cleanup tmpdir
 
-test_init :: TestEnv -> Test
-test_init env = "git-annex init" ~: TestCase $ innewrepo env $ do
+test_init :: TestEnv -> Assertion
+test_init env = innewrepo env $ do
 	git_annex env "init" [reponame] @? "init failed"
 	handleforcedirect env
   where
 	reponame = "test repo"
 
-test_add :: TestEnv -> Test
-test_add env = "git-annex add" ~: TestList [basic, sha1dup, subdirs]
-  where
-	-- this test case runs in the main repo, to set up a basic
-	-- annexed file that later tests will use
-	basic = TestCase $ inmainrepo env $ do
-		writeFile annexedfile $ content annexedfile
-		git_annex env "add" [annexedfile] @? "add failed"
-		annexed_present annexedfile
-		writeFile sha1annexedfile $ content sha1annexedfile
-		git_annex env "add" [sha1annexedfile, "--backend=SHA1"] @? "add with SHA1 failed"
-		annexed_present sha1annexedfile
-		checkbackend sha1annexedfile backendSHA1
-		writeFile wormannexedfile $ content wormannexedfile
-		git_annex env "add" [wormannexedfile, "--backend=WORM"] @? "add with WORM failed"
-		annexed_present wormannexedfile
-		checkbackend wormannexedfile backendWORM
-		boolSystem "git" [Params "rm --force -q", File wormannexedfile] @? "git rm failed"
-		writeFile ingitfile $ content ingitfile
-		boolSystem "git" [Param "add", File ingitfile] @? "git add failed"
-		boolSystem "git" [Params "commit -q -m commit"] @? "git commit failed"
-		git_annex env "add" [ingitfile] @? "add ingitfile should be no-op"
-		unannexed ingitfile
-	sha1dup = TestCase $ intmpclonerepo env $ do
-		writeFile sha1annexedfiledup $ content sha1annexedfiledup
-		git_annex env "add" [sha1annexedfiledup, "--backend=SHA1"] @? "add of second file with same SHA1 failed"
-		annexed_present sha1annexedfiledup
-		annexed_present sha1annexedfile
-	subdirs = TestCase $ intmpclonerepo env $ do
-		createDirectory "dir"
-		writeFile ("dir" </> "foo") $ content annexedfile
-		git_annex env "add" ["dir"] @? "add of subdir failed"
-		createDirectory "dir2"
-		writeFile ("dir2" </> "foo") $ content annexedfile
+-- this test case runs in the main repo, to set up a basic
+-- annexed file that later tests will use
+test_add :: TestEnv -> Assertion
+test_add env = inmainrepo env $ do
+	writeFile annexedfile $ content annexedfile
+	git_annex env "add" [annexedfile] @? "add failed"
+	annexed_present annexedfile
+	writeFile sha1annexedfile $ content sha1annexedfile
+	git_annex env "add" [sha1annexedfile, "--backend=SHA1"] @? "add with SHA1 failed"
+	annexed_present sha1annexedfile
+	checkbackend sha1annexedfile backendSHA1
+	writeFile wormannexedfile $ content wormannexedfile
+	git_annex env "add" [wormannexedfile, "--backend=WORM"] @? "add with WORM failed"
+	annexed_present wormannexedfile
+	checkbackend wormannexedfile backendWORM
+	ifM (annexeval Config.isDirect)
+		( do
+			boolSystem "rm" [Params "-f", File wormannexedfile] @? "rm failed"
+			writeFile ingitfile $ content ingitfile
+			not <$> boolSystem "git" [Param "add", File ingitfile] @? "git add failed to fail in direct mode"
+			boolSystem "rm" [Params "-f", File ingitfile] @? "rm failed"
+			git_annex env "sync" [] @? "sync failed"
+		, do
+			boolSystem "git" [Params "rm --force -q", File wormannexedfile] @? "git rm failed"
+			writeFile ingitfile $ content ingitfile
+			boolSystem "git" [Param "add", File ingitfile] @? "git add failed"
+			boolSystem "git" [Params "commit -q -m commit"] @? "git commit failed"
+			git_annex env "add" [ingitfile] @? "add ingitfile should be no-op"
+			unannexed ingitfile
+		)
+
+test_add_sha1dup :: TestEnv -> Assertion
+test_add_sha1dup env = intmpclonerepo env $ do
+	writeFile sha1annexedfiledup $ content sha1annexedfiledup
+	git_annex env "add" [sha1annexedfiledup, "--backend=SHA1"] @? "add of second file with same SHA1 failed"
+	annexed_present sha1annexedfiledup
+	annexed_present sha1annexedfile
+
+test_add_subdirs :: TestEnv -> Assertion
+test_add_subdirs env = intmpclonerepo env $ do
+	createDirectory "dir"
+	writeFile ("dir" </> "foo") $ content annexedfile
+	git_annex env "add" ["dir"] @? "add of subdir failed"
+	createDirectory "dir2"
+	writeFile ("dir2" </> "foo") $ content annexedfile
 #ifndef mingw32_HOST_OS
-		{- This does not work on Windows, for whatever reason. -}
-		setCurrentDirectory "dir"
-		git_annex env "add" [".." </> "dir2"] @? "add of ../subdir failed"
+	{- This does not work on Windows, for whatever reason. -}
+	setCurrentDirectory "dir"
+	git_annex env "add" [".." </> "dir2"] @? "add of ../subdir failed"
 #endif
 
-test_reinject :: TestEnv -> Test
-test_reinject env = "git-annex reinject/fromkey" ~: TestCase $ intmpclonerepoInDirect env $ do
+test_reinject :: TestEnv -> Assertion
+test_reinject env = intmpclonerepoInDirect env $ do
 	git_annex env "drop" ["--force", sha1annexedfile] @? "drop failed"
 	writeFile tmp $ content sha1annexedfile
 	r <- annexeval $ Types.Backend.getKey backendSHA1 $
@@ -251,53 +256,57 @@ test_reinject env = "git-annex reinject/fromkey" ~: TestCase $ intmpclonerepoInD
   where
 	tmp = "tmpfile"
 
-test_unannex :: TestEnv -> Test
-test_unannex env = "git-annex unannex" ~: TestList [nocopy, withcopy]
-  where
-	nocopy = "no content" ~: intmpclonerepo env $ do
-		annexed_notpresent annexedfile
-		git_annex env "unannex" [annexedfile] @? "unannex failed with no copy"
-		annexed_notpresent annexedfile
-	withcopy = "with content" ~: intmpclonerepo env $ do
-		git_annex env "get" [annexedfile] @? "get failed"
-		annexed_present annexedfile
-		git_annex env "unannex" [annexedfile, sha1annexedfile] @? "unannex failed"
-		unannexed annexedfile
-		git_annex env "unannex" [annexedfile] @? "unannex failed on non-annexed file"
-		unannexed annexedfile
+test_unannex_nocopy :: TestEnv -> Assertion
+test_unannex_nocopy env = intmpclonerepo env $ do
+	annexed_notpresent annexedfile
+	git_annex env "unannex" [annexedfile] @? "unannex failed with no copy"
+	annexed_notpresent annexedfile
+
+test_unannex_withcopy :: TestEnv -> Assertion
+test_unannex_withcopy env = intmpclonerepo env $ do
+	git_annex env "get" [annexedfile] @? "get failed"
+	annexed_present annexedfile
+	git_annex env "unannex" [annexedfile, sha1annexedfile] @? "unannex failed"
+	unannexed annexedfile
+	git_annex env "unannex" [annexedfile] @? "unannex failed on non-annexed file"
+	unannexed annexedfile
+	unlessM (annexeval Config.isDirect) $ do
 		git_annex env "unannex" [ingitfile] @? "unannex ingitfile should be no-op"
 		unannexed ingitfile
 
-test_drop :: TestEnv -> Test
-test_drop env = "git-annex drop" ~: TestList [noremote, withremote, untrustedremote]
-  where
-	noremote = "no remotes" ~: TestCase $ intmpclonerepo env $ do
-		git_annex env "get" [annexedfile] @? "get failed"
-		boolSystem "git" [Params "remote rm origin"]
-			@? "git remote rm origin failed"
-		not <$> git_annex env "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of file"
-		annexed_present annexedfile
-		git_annex env "drop" ["--force", annexedfile] @? "drop --force failed"
-		annexed_notpresent annexedfile
-		git_annex env "drop" [annexedfile] @? "drop of dropped file failed"
+test_drop_noremote :: TestEnv -> Assertion
+test_drop_noremote env = intmpclonerepo env $ do
+	git_annex env "get" [annexedfile] @? "get failed"
+	boolSystem "git" [Params "remote rm origin"]
+		@? "git remote rm origin failed"
+	not <$> git_annex env "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of file"
+	annexed_present annexedfile
+	git_annex env "drop" ["--force", annexedfile] @? "drop --force failed"
+	annexed_notpresent annexedfile
+	git_annex env "drop" [annexedfile] @? "drop of dropped file failed"
+	unlessM (annexeval Config.isDirect) $ do
 		git_annex env "drop" [ingitfile] @? "drop ingitfile should be no-op"
 		unannexed ingitfile
-	withremote = "with remote" ~: TestCase $ intmpclonerepo env $ do
-		git_annex env "get" [annexedfile] @? "get failed"
-		annexed_present annexedfile
-		git_annex env "drop" [annexedfile] @? "drop failed though origin has copy"
-		annexed_notpresent annexedfile
-		inmainrepo env $ annexed_present annexedfile
-	untrustedremote = "untrusted remote" ~: TestCase $ intmpclonerepo env $ do
-		git_annex env "untrust" ["origin"] @? "untrust of origin failed"
-		git_annex env "get" [annexedfile] @? "get failed"
-		annexed_present annexedfile
-		not <$> git_annex env "drop" [annexedfile] @? "drop wrongly suceeded with only an untrusted copy of the file"
-		annexed_present annexedfile
-		inmainrepo env $ annexed_present annexedfile
-
-test_get :: TestEnv -> Test
-test_get env = "git-annex get" ~: TestCase $ intmpclonerepo env $ do
+
+test_drop_withremote :: TestEnv -> Assertion
+test_drop_withremote env = intmpclonerepo env $ do
+	git_annex env "get" [annexedfile] @? "get failed"
+	annexed_present annexedfile
+	git_annex env "drop" [annexedfile] @? "drop failed though origin has copy"
+	annexed_notpresent annexedfile
+	inmainrepo env $ annexed_present annexedfile
+
+test_drop_untrustedremote :: TestEnv -> Assertion
+test_drop_untrustedremote env = intmpclonerepo env $ do
+	git_annex env "untrust" ["origin"] @? "untrust of origin failed"
+	git_annex env "get" [annexedfile] @? "get failed"
+	annexed_present annexedfile
+	not <$> git_annex env "drop" [annexedfile] @? "drop wrongly suceeded with only an untrusted copy of the file"
+	annexed_present annexedfile
+	inmainrepo env $ annexed_present annexedfile
+
+test_get :: TestEnv -> Assertion
+test_get env = intmpclonerepo env $ do
 	inmainrepo env $ annexed_present annexedfile
 	annexed_notpresent annexedfile
 	git_annex env "get" [annexedfile] @? "get of file failed"
@@ -306,14 +315,15 @@ test_get env = "git-annex get" ~: TestCase $ intmpclonerepo env $ do
 	git_annex env "get" [annexedfile] @? "get of file already here failed"
 	inmainrepo env $ annexed_present annexedfile
 	annexed_present annexedfile
-	inmainrepo env $ unannexed ingitfile
-	unannexed ingitfile
-	git_annex env "get" [ingitfile] @? "get ingitfile should be no-op"
-	inmainrepo env $ unannexed ingitfile
-	unannexed ingitfile
-
-test_move :: TestEnv -> Test
-test_move env = "git-annex move" ~: TestCase $ intmpclonerepo env $ do
+	unlessM (annexeval Config.isDirect) $ do
+		inmainrepo env $ unannexed ingitfile
+		unannexed ingitfile
+		git_annex env "get" [ingitfile] @? "get ingitfile should be no-op"
+		inmainrepo env $ unannexed ingitfile
+		unannexed ingitfile
+
+test_move :: TestEnv -> Assertion
+test_move env = intmpclonerepo env $ do
 	annexed_notpresent annexedfile
 	inmainrepo env $ annexed_present annexedfile
 	git_annex env "move" ["--from", "origin", annexedfile] @? "move --from of file failed"
@@ -328,17 +338,18 @@ test_move env = "git-annex move" ~: TestCase $ intmpclonerepo env $ do
 	git_annex env "move" ["--to", "origin", annexedfile] @? "move --to of file already there failed"
 	inmainrepo env $ annexed_present annexedfile
 	annexed_notpresent annexedfile
-	unannexed ingitfile
-	inmainrepo env $ unannexed ingitfile
-	git_annex env "move" ["--to", "origin", ingitfile] @? "move of ingitfile should be no-op"
-	unannexed ingitfile
-	inmainrepo env $ unannexed ingitfile
-	git_annex env "move" ["--from", "origin", ingitfile] @? "move of ingitfile should be no-op"
-	unannexed ingitfile
-	inmainrepo env $ unannexed ingitfile
-
-test_copy :: TestEnv -> Test
-test_copy env = "git-annex copy" ~: TestCase $ intmpclonerepo env $ do
+	unlessM (annexeval Config.isDirect) $ do
+		unannexed ingitfile
+		inmainrepo env $ unannexed ingitfile
+		git_annex env "move" ["--to", "origin", ingitfile] @? "move of ingitfile should be no-op"
+		unannexed ingitfile
+		inmainrepo env $ unannexed ingitfile
+		git_annex env "move" ["--from", "origin", ingitfile] @? "move of ingitfile should be no-op"
+		unannexed ingitfile
+		inmainrepo env $ unannexed ingitfile
+
+test_copy :: TestEnv -> Assertion
+test_copy env = intmpclonerepo env $ do
 	annexed_notpresent annexedfile
 	inmainrepo env $ annexed_present annexedfile
 	git_annex env "copy" ["--from", "origin", annexedfile] @? "copy --from of file failed"
@@ -353,17 +364,18 @@ test_copy env = "git-annex copy" ~: TestCase $ intmpclonerepo env $ do
 	git_annex env "move" ["--to", "origin", annexedfile] @? "move --to of file already there failed"
 	annexed_notpresent annexedfile
 	inmainrepo env $ annexed_present annexedfile
-	unannexed ingitfile
-	inmainrepo env $ unannexed ingitfile
-	git_annex env "copy" ["--to", "origin", ingitfile] @? "copy of ingitfile should be no-op"
-	unannexed ingitfile
-	inmainrepo env $ unannexed ingitfile
-	git_annex env "copy" ["--from", "origin", ingitfile] @? "copy of ingitfile should be no-op"
-	checkregularfile ingitfile
-	checkcontent ingitfile
-
-test_preferred_content :: TestEnv -> Test
-test_preferred_content env = "git-annex preferred-content" ~: TestCase $ intmpclonerepo env $ do
+	unlessM (annexeval Config.isDirect) $ do
+		unannexed ingitfile
+		inmainrepo env $ unannexed ingitfile
+		git_annex env "copy" ["--to", "origin", ingitfile] @? "copy of ingitfile should be no-op"
+		unannexed ingitfile
+		inmainrepo env $ unannexed ingitfile
+		git_annex env "copy" ["--from", "origin", ingitfile] @? "copy of ingitfile should be no-op"
+		checkregularfile ingitfile
+		checkcontent ingitfile
+
+test_preferred_content :: TestEnv -> Assertion
+test_preferred_content env = intmpclonerepo env $ do
 	annexed_notpresent annexedfile
 	-- get --auto only looks at numcopies when preferred content is not
 	-- set, and with 1 copy existing, does not get the file.
@@ -396,8 +408,8 @@ test_preferred_content env = "git-annex preferred-content" ~: TestCase $ intmpcl
 	git_annex env "get" ["--auto", annexedfile] @? "get --auto of file failed with exclude=*"
 	annexed_notpresent annexedfile
 
-test_lock :: TestEnv -> Test
-test_lock env = "git-annex unlock/lock" ~: intmpclonerepoInDirect env $ do
+test_lock :: TestEnv -> Assertion
+test_lock env = intmpclonerepoInDirect env $ do
 	-- regression test: unlock of not present file should skip it
 	annexed_notpresent annexedfile
 	not <$> git_annex env "unlock" [annexedfile] @? "unlock failed to fail with not present file"
@@ -423,9 +435,14 @@ test_lock env = "git-annex unlock/lock" ~: intmpclonerepoInDirect env $ do
 	r' <- git_annex env "drop" [annexedfile]
 	not r' @? "drop wrongly succeeded with no known copy of modified file"
 
-test_edit :: TestEnv -> Test
-test_edit env = "git-annex edit/commit" ~: TestList [t False, t True]
-  where t precommit = TestCase $ intmpclonerepoInDirect env $ do
+test_edit :: TestEnv -> Assertion
+test_edit = test_edit' False
+
+test_edit_precommit :: TestEnv -> Assertion
+test_edit_precommit = test_edit' True
+
+test_edit' :: Bool -> TestEnv -> Assertion
+test_edit' precommit env = intmpclonerepoInDirect env $ do
 	git_annex env "get" [annexedfile] @? "get of file failed"
 	annexed_present annexedfile
 	git_annex env "edit" [annexedfile] @? "edit failed"
@@ -443,8 +460,8 @@ test_edit env = "git-annex edit/commit" ~: TestList [t False, t True]
 	assertEqual "content of modified file" c (changedcontent annexedfile)
 	not <$> git_annex env "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of modified file"
 
-test_fix :: TestEnv -> Test
-test_fix env = "git-annex fix" ~: intmpclonerepoInDirect env $ do
+test_fix :: TestEnv -> Assertion
+test_fix env = intmpclonerepoInDirect env $ do
 	annexed_notpresent annexedfile
 	git_annex env "fix" [annexedfile] @? "fix of not present failed"
 	annexed_notpresent annexedfile
@@ -463,8 +480,8 @@ test_fix env = "git-annex fix" ~: intmpclonerepoInDirect env $ do
 	subdir = "s"
 	newfile = subdir ++ "/" ++ annexedfile
 
-test_trust :: TestEnv -> Test
-test_trust env = "git-annex trust/untrust/semitrust/dead" ~: intmpclonerepo env $ do
+test_trust :: TestEnv -> Assertion
+test_trust env = intmpclonerepo env $ do
 	git_annex env "trust" [repo] @? "trust failed"
 	trustcheck Logs.Trust.Trusted "trusted 1"
 	git_annex env "trust" [repo] @? "trust of trusted failed"
@@ -490,33 +507,15 @@ test_trust env = "git-annex trust/untrust/semitrust/dead" ~: intmpclonerepo env
 			return $ u `elem` l
 		assertBool msg present
 
-test_fsck :: TestEnv -> Test
-test_fsck env = "git-annex fsck" ~: TestList [basicfsck, barefsck, withlocaluntrusted, withremoteuntrusted]
+test_fsck_basic :: TestEnv -> Assertion
+test_fsck_basic env = intmpclonerepo env $ do
+	git_annex env "fsck" [] @? "fsck failed"
+	boolSystem "git" [Params "config annex.numcopies 2"] @? "git config failed"
+	fsck_should_fail env "numcopies unsatisfied"
+	boolSystem "git" [Params "config annex.numcopies 1"] @? "git config failed"
+	corrupt annexedfile
+	corrupt sha1annexedfile
   where
-	basicfsck = TestCase $ intmpclonerepo env $ do
-		git_annex env "fsck" [] @? "fsck failed"
-		boolSystem "git" [Params "config annex.numcopies 2"] @? "git config failed"
-		fsck_should_fail "numcopies unsatisfied"
-		boolSystem "git" [Params "config annex.numcopies 1"] @? "git config failed"
-		corrupt annexedfile
-		corrupt sha1annexedfile
-	barefsck = TestCase $ intmpbareclonerepo env $ do
-		git_annex env "fsck" [] @? "fsck failed"
-	withlocaluntrusted = TestCase $ intmpclonerepo env $ do
-		git_annex env "get" [annexedfile] @? "get failed"
-		git_annex env "untrust" ["origin"] @? "untrust of origin repo failed"
-		git_annex env "untrust" ["."] @? "untrust of current repo failed"
-		fsck_should_fail "content only available in untrusted (current) repository"
-		git_annex env "trust" ["."] @? "trust of current repo failed"
-		git_annex env "fsck" [annexedfile] @? "fsck failed on file present in trusted repo"
-	withremoteuntrusted = TestCase $ intmpclonerepo env $ do
-		boolSystem "git" [Params "config annex.numcopies 2"] @? "git config failed"
-		git_annex env "get" [annexedfile] @? "get failed"
-		git_annex env "get" [sha1annexedfile] @? "get failed"
-		git_annex env "fsck" [] @? "fsck failed with numcopies=2 and 2 copies"
-		git_annex env "untrust" ["origin"] @? "untrust of origin failed"
-		fsck_should_fail "content not replicated to enough non-untrusted repositories"
-
 	corrupt f = do
 		git_annex env "get" [f] @? "get of file failed"
 		Utility.FileMode.allowWrite f
@@ -526,12 +525,41 @@ test_fsck env = "git-annex fsck" ~: TestList [basicfsck, barefsck, withlocaluntr
 			, not <$> git_annex env "fsck" [] @? "fsck failed to fail with corrupted file content"
 			)
 		git_annex env "fsck" [] @? "fsck unexpectedly failed again; previous one did not fix problem with " ++ f
-	fsck_should_fail m = do
-		not <$> git_annex env "fsck" [] @? "fsck failed to fail with " ++ m
 
-test_migrate :: TestEnv -> Test
-test_migrate env = "git-annex migrate" ~: TestList [t False, t True]
-  where t usegitattributes = TestCase $ intmpclonerepoInDirect env $ do
+test_fsck_bare :: TestEnv -> Assertion
+test_fsck_bare env = intmpbareclonerepo env $ do
+	git_annex env "fsck" [] @? "fsck failed"
+
+test_fsck_localuntrusted :: TestEnv -> Assertion
+test_fsck_localuntrusted env = intmpclonerepo env $ do
+	git_annex env "get" [annexedfile] @? "get failed"
+	git_annex env "untrust" ["origin"] @? "untrust of origin repo failed"
+	git_annex env "untrust" ["."] @? "untrust of current repo failed"
+	fsck_should_fail env "content only available in untrusted (current) repository"
+	git_annex env "trust" ["."] @? "trust of current repo failed"
+	git_annex env "fsck" [annexedfile] @? "fsck failed on file present in trusted repo"
+
+test_fsck_remoteuntrusted :: TestEnv -> Assertion
+test_fsck_remoteuntrusted env = intmpclonerepo env $ do
+	boolSystem "git" [Params "config annex.numcopies 2"] @? "git config failed"
+	git_annex env "get" [annexedfile] @? "get failed"
+	git_annex env "get" [sha1annexedfile] @? "get failed"
+	git_annex env "fsck" [] @? "fsck failed with numcopies=2 and 2 copies"
+	git_annex env "untrust" ["origin"] @? "untrust of origin failed"
+	fsck_should_fail env "content not replicated to enough non-untrusted repositories"
+
+fsck_should_fail :: TestEnv -> String -> Assertion
+fsck_should_fail env m = not <$> git_annex env "fsck" []
+	@? "fsck failed to fail with " ++ m
+
+test_migrate :: TestEnv -> Assertion
+test_migrate = test_migrate' False
+
+test_migrate_via_gitattributes :: TestEnv -> Assertion
+test_migrate_via_gitattributes = test_migrate' True
+
+test_migrate' :: Bool -> TestEnv -> Assertion
+test_migrate' usegitattributes env = intmpclonerepoInDirect env $ do
 	annexed_notpresent annexedfile
 	annexed_notpresent sha1annexedfile
 	git_annex env "migrate" [annexedfile] @? "migrate of not present failed"
@@ -568,9 +596,9 @@ test_migrate env = "git-annex migrate" ~: TestList [t False, t True]
 	checkbackend annexedfile backendSHA256
 	checkbackend sha1annexedfile backendSHA256
 
-test_unused :: TestEnv -> Test
+test_unused :: TestEnv -> Assertion
 -- This test is broken in direct mode
-test_unused env = "git-annex unused/dropunused" ~: intmpclonerepoInDirect env $ do
+test_unused env = intmpclonerepoInDirect env $ do
 	-- keys have to be looked up before files are removed
 	annexedfilekey <- annexeval $ findkey annexedfile
 	sha1annexedfilekey <- annexeval $ findkey sha1annexedfile
@@ -640,13 +668,13 @@ test_unused env = "git-annex unused/dropunused" ~: intmpclonerepoInDirect env $
 		r <- Backend.lookupFile f
 		return $ fst $ fromJust r
 
-test_describe :: TestEnv -> Test
-test_describe env = "git-annex describe" ~: intmpclonerepo env $ do
+test_describe :: TestEnv -> Assertion
+test_describe env = intmpclonerepo env $ do
 	git_annex env "describe" [".", "this repo"] @? "describe 1 failed"
 	git_annex env "describe" ["origin", "origin repo"] @? "describe 2 failed"
 
-test_find :: TestEnv -> Test
-test_find env = "git-annex find" ~: intmpclonerepo env $ do
+test_find :: TestEnv -> Assertion
+test_find env = intmpclonerepo env $ do
 	annexed_notpresent annexedfile
 	git_annex_expectoutput env "find" [] []
 	git_annex env "get" [annexedfile] @? "get failed"
@@ -668,23 +696,23 @@ test_find env = "git-annex find" ~: intmpclonerepo env $ do
 	git_annex_expectoutput env "find" ["--include", "*", "--exclude", annexedfile, "--exclude", sha1annexedfile] ["dir/subfile"]
 	git_annex_expectoutput env "find" ["--exclude", "*"] []
 
-test_merge :: TestEnv -> Test
-test_merge env = "git-annex merge" ~: intmpclonerepo env $ do
+test_merge :: TestEnv -> Assertion
+test_merge env = intmpclonerepo env $ do
 	git_annex env "merge" [] @? "merge failed"
 
-test_status :: TestEnv -> Test
-test_status env = "git-annex status" ~: intmpclonerepo env $ do
-	json <- git_annex_output env "status" ["--json"]
+test_info :: TestEnv -> Assertion
+test_info env = intmpclonerepo env $ do
+	json <- git_annex_output env "info" ["--json"]
 	case Text.JSON.decodeStrict json :: Text.JSON.Result (Text.JSON.JSObject Text.JSON.JSValue) of
 		Text.JSON.Ok _ -> return ()
 		Text.JSON.Error e -> assertFailure e
 
-test_version :: TestEnv -> Test
-test_version env = "git-annex version" ~: intmpclonerepo env $ do
+test_version :: TestEnv -> Assertion
+test_version env = intmpclonerepo env $ do
 	git_annex env "version" [] @? "version failed"
 
-test_sync :: TestEnv -> Test
-test_sync env = "git-annex sync" ~: intmpclonerepo env $ do
+test_sync :: TestEnv -> Assertion
+test_sync env = intmpclonerepo env $ do
 	git_annex env "sync" [] @? "sync failed"
 	{- Regression test for bug fixed in 
 	 - 7b0970b340d7faeb745c666146c7f701ec71808f, where in direct mode
@@ -693,8 +721,8 @@ test_sync env = "git-annex sync" ~: intmpclonerepo env $ do
 
 {- Regression test for union merge bug fixed in
  - 0214e0fb175a608a49b812d81b4632c081f63027 -}
-test_union_merge_regression :: TestEnv -> Test
-test_union_merge_regression env = "union merge regression" ~:
+test_union_merge_regression :: TestEnv -> Assertion
+test_union_merge_regression env =
 	{- We need 3 repos to see this bug. -}
 	withtmpclonerepo env False $ \r1 -> do
 		withtmpclonerepo env False $ \r2 -> do
@@ -720,45 +748,47 @@ test_union_merge_regression env = "union merge regression" ~:
 					 - thought the file was still in r2 -}
 					git_annex_expectoutput env "find" ["--in", "r2"] []
 
-test_conflict_resolution :: TestEnv -> Test
-test_conflict_resolution env = "automatic conflict resolution" ~:
-	TestList [movein_bug, check_mixed_conflict True, check_mixed_conflict False]
+{- Regression test for the automatic conflict resolution bug fixed
+ - in f4ba19f2b8a76a1676da7bb5850baa40d9c388e2. -}
+test_conflict_resolution_movein_bug :: TestEnv -> Assertion
+test_conflict_resolution_movein_bug env = withtmpclonerepo env False $ \r1 -> do
+	withtmpclonerepo env False $ \r2 -> do
+		let rname r = if r == r1 then "r1" else "r2"
+		forM_ [r1, r2] $ \r -> indir env r $ do
+			{- Get all files, see check below. -}
+			git_annex env "get" [] @? "get failed"
+		pair env r1 r2
+		forM_ [r1, r2] $ \r -> indir env r $ do
+			{- Set up a conflict. -}
+			let newcontent = content annexedfile ++ rname r
+			ifM (annexeval Config.isDirect)
+				( writeFile annexedfile newcontent
+				, do
+					git_annex env "unlock" [annexedfile] @? "unlock failed"		
+					writeFile annexedfile newcontent
+				)
+		{- Sync twice in r1 so it gets the conflict resolution
+		 - update from r2 -}
+		forM_ [r1, r2, r1] $ \r -> indir env r $ do
+			git_annex env "sync" ["--force"] @? "sync failed in " ++ rname r
+		{- After the sync, it should be possible to get all
+		 - files. This includes both sides of the conflict,
+		 - although the filenames are not easily predictable.
+		 -
+		 - The bug caused, in direct mode, one repo to
+		 - be missing the content of the file that had
+		 - been put in it. -}
+		forM_ [r1, r2] $ \r -> indir env r $ do
+		 	git_annex env "get" [] @? "unable to get all files after merge conflict resolution in " ++ rname r
+
+{- Check merge conflict resolution when one side is an annexed
+ - file, and the other is a directory. -}
+test_mixed_conflict_resolution :: TestEnv -> Assertion
+test_mixed_conflict_resolution env = do
+	check_mixed_conflict True
+	check_mixed_conflict False
   where
-	{- Regression test for the automatic conflict resolution bug fixed
-	 - in f4ba19f2b8a76a1676da7bb5850baa40d9c388e2. -}
-	movein_bug = TestCase $ withtmpclonerepo env False $ \r1 -> do
-		withtmpclonerepo env False $ \r2 -> do
-			let rname r = if r == r1 then "r1" else "r2"
-			forM_ [r1, r2] $ \r -> indir env r $ do
-				{- Get all files, see check below. -}
-				git_annex env "get" [] @? "get failed"
-			pair r1 r2
-			forM_ [r1, r2] $ \r -> indir env r $ do
-				{- Set up a conflict. -}
-				let newcontent = content annexedfile ++ rname r
-				ifM (annexeval Config.isDirect)
-					( writeFile annexedfile newcontent
-					, do
-						git_annex env "unlock" [annexedfile] @? "unlock failed"		
-						writeFile annexedfile newcontent
-					)
-			{- Sync twice in r1 so it gets the conflict resolution
-			 - update from r2 -}
-			forM_ [r1, r2, r1] $ \r -> indir env r $ do
-				git_annex env "sync" [] @? "sync failed in " ++ rname r
-			{- After the sync, it should be possible to get all
-			 - files. This includes both sides of the conflict,
-			 - although the filenames are not easily predictable.
-			 -
-			 - The bug caused, in direct mode, one repo to
-			 - be missing the content of the file that had
-			 - been put in it. -}
-			forM_ [r1, r2] $ \r -> indir env r $ do
-			 	git_annex env "get" [] @? "unable to get all files after merge conflict resolution in " ++ rname r
-
-	{- Check merge conflict resolution when one side is an annexed
-	 - file, and the other is a directory. -}
-	check_mixed_conflict inr1 = TestCase $ withtmpclonerepo env False $ \r1 ->
+	check_mixed_conflict inr1 = withtmpclonerepo env False $ \r1 ->
 		withtmpclonerepo env False $ \r2 -> do
 			indir env r1 $ do
 				writeFile conflictor "conflictor"
@@ -769,50 +799,59 @@ test_conflict_resolution env = "automatic conflict resolution" ~:
 				writeFile (conflictor </> "subfile") "subfile"
 				git_annex env "add" [conflictor] @? "add conflicter failed"
 				git_annex env "sync" [] @? "sync failed"
-			pair r1 r2
+			pair env r1 r2
 			let r = if inr1 then r1 else r2
 			indir env r $ do
 				git_annex env "sync" [] @? "sync failed in mixed conflict"
+			checkmerge r1
+			checkmerge r2
 	  where
 		conflictor = "conflictor"
-
-	{- Set up repos as remotes of each other;
-	 - remove origin since we're going to sync
-	 - some changes to a file. -}
-	pair r1 r2 = forM_ [r1, r2] $ \r -> indir env r $ do
-		when (r /= r1) $
-			boolSystem "git" [Params "remote add r1", File ("../../" ++ r1)] @? "remote add"
-		when (r /= r2) $
-			boolSystem "git" [Params "remote add r2", File ("../../" ++ r2)] @? "remote add"
-		boolSystem "git" [Params "remote rm origin"] @? "remote rm"
-
-test_map :: TestEnv -> Test
-test_map env = "git-annex map" ~: intmpclonerepo env $ do
+		variantprefix = conflictor ++ ".variant"
+		checkmerge d = do
+			doesDirectoryExist (d </> conflictor) @? (d ++ " conflictor directory missing")
+			(any (variantprefix `isPrefixOf`) 
+				<$> getDirectoryContents d)
+				@? (d ++ "conflictor file missing")
+
+{- Set up repos as remotes of each other;
+ - remove origin since we're going to sync
+ - some changes to a file. -}
+pair :: TestEnv -> FilePath -> FilePath -> Assertion
+pair env r1 r2 = forM_ [r1, r2] $ \r -> indir env r $ do
+	when (r /= r1) $
+		boolSystem "git" [Params "remote add r1", File ("../../" ++ r1)] @? "remote add"
+	when (r /= r2) $
+		boolSystem "git" [Params "remote add r2", File ("../../" ++ r2)] @? "remote add"
+	boolSystem "git" [Params "remote rm origin"] @? "remote rm"
+
+test_map :: TestEnv -> Assertion
+test_map env = intmpclonerepo env $ do
 	-- set descriptions, that will be looked for in the map
 	git_annex env "describe" [".", "this repo"] @? "describe 1 failed"
 	git_annex env "describe" ["origin", "origin repo"] @? "describe 2 failed"
 	-- --fast avoids it running graphviz, not a build dependency
 	git_annex env "map" ["--fast"] @? "map failed"
 
-test_uninit :: TestEnv -> Test
-test_uninit env = "git-annex uninit" ~: TestList [inbranch, normal]
-  where
-  	inbranch = "in branch" ~: intmpclonerepoInDirect env $ do
-		boolSystem "git" [Params "checkout git-annex"] @? "git checkout git-annex"
-		not <$> git_annex env "uninit" [] @? "uninit failed to fail when git-annex branch was checked out"
-	normal = "normal" ~: intmpclonerepo env $ do
-		git_annex env "get" [] @? "get failed"
-		annexed_present annexedfile
-		_ <- git_annex env "uninit" [] -- exit status not checked; does abnormal exit
-		checkregularfile annexedfile
-		doesDirectoryExist ".git" @? ".git vanished in uninit"
-
-test_upgrade :: TestEnv -> Test
-test_upgrade env = "git-annex upgrade" ~: intmpclonerepo env $ do
+test_uninit :: TestEnv -> Assertion
+test_uninit env = intmpclonerepo env $ do
+	git_annex env "get" [] @? "get failed"
+	annexed_present annexedfile
+	_ <- git_annex env "uninit" [] -- exit status not checked; does abnormal exit
+	checkregularfile annexedfile
+	doesDirectoryExist ".git" @? ".git vanished in uninit"
+
+test_uninit_inbranch :: TestEnv -> Assertion
+test_uninit_inbranch env = intmpclonerepoInDirect env $ do
+	boolSystem "git" [Params "checkout git-annex"] @? "git checkout git-annex"
+	not <$> git_annex env "uninit" [] @? "uninit failed to fail when git-annex branch was checked out"
+
+test_upgrade :: TestEnv -> Assertion
+test_upgrade env = intmpclonerepo env $ do
 	git_annex env "upgrade" [] @? "upgrade from same version failed"
 
-test_whereis :: TestEnv -> Test
-test_whereis env = "git-annex whereis" ~: intmpclonerepo env $ do
+test_whereis :: TestEnv -> Assertion
+test_whereis env = intmpclonerepo env $ do
 	annexed_notpresent annexedfile
 	git_annex env "whereis" [annexedfile] @? "whereis on non-present file failed"
 	git_annex env "untrust" ["origin"] @? "untrust failed"
@@ -821,8 +860,8 @@ test_whereis env = "git-annex whereis" ~: intmpclonerepo env $ do
 	annexed_present annexedfile
 	git_annex env "whereis" [annexedfile] @? "whereis on present file failed"
 
-test_hook_remote :: TestEnv -> Test
-test_hook_remote env = "git-annex hook remote" ~: intmpclonerepo env $ do
+test_hook_remote :: TestEnv -> Assertion
+test_hook_remote env = intmpclonerepo env $ do
 #ifndef mingw32_HOST_OS
 	git_annex env "initremote" (words "foo type=hook encryption=none hooktype=foo") @? "initremote failed"
 	createDirectory dir
@@ -854,8 +893,8 @@ test_hook_remote env = "git-annex hook remote" ~: intmpclonerepo env $ do
 	noop
 #endif
 
-test_directory_remote :: TestEnv -> Test
-test_directory_remote env = "git-annex directory remote" ~: intmpclonerepo env $ do
+test_directory_remote :: TestEnv -> Assertion
+test_directory_remote env = intmpclonerepo env $ do
 	createDirectory "dir"
 	git_annex env "initremote" (words $ "foo type=directory encryption=none directory=dir") @? "initremote failed"
 	git_annex env "get" [annexedfile] @? "get of file failed"
@@ -869,8 +908,8 @@ test_directory_remote env = "git-annex directory remote" ~: intmpclonerepo env $
 	not <$> git_annex env "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
 	annexed_present annexedfile
 
-test_rsync_remote :: TestEnv -> Test
-test_rsync_remote env = "git-annex rsync remote" ~: intmpclonerepo env $ do
+test_rsync_remote :: TestEnv -> Assertion
+test_rsync_remote env = intmpclonerepo env $ do
 #ifndef mingw32_HOST_OS
 	createDirectory "dir"
 	git_annex env "initremote" (words $ "foo type=rsync encryption=none rsyncurl=dir") @? "initremote failed"
@@ -889,8 +928,8 @@ test_rsync_remote env = "git-annex rsync remote" ~: intmpclonerepo env $ do
 	noop
 #endif
 
-test_bup_remote :: TestEnv -> Test
-test_bup_remote env = "git-annex bup remote" ~: intmpclonerepo env $ when Build.SysConfig.bup $ do
+test_bup_remote :: TestEnv -> Assertion
+test_bup_remote env = intmpclonerepo env $ when Build.SysConfig.bup $ do
 	dir <- absPath "dir" -- bup special remote needs an absolute path
 	createDirectory dir
 	git_annex env "initremote" (words $ "foo type=bup encryption=none buprepo="++dir) @? "initremote failed"
@@ -906,47 +945,50 @@ test_bup_remote env = "git-annex bup remote" ~: intmpclonerepo env $ when Build.
 	annexed_present annexedfile
 
 -- gpg is not a build dependency, so only test when it's available
-test_crypto :: TestEnv -> Test
+test_crypto :: TestEnv -> Assertion
 #ifndef mingw32_HOST_OS
-test_crypto env = "git-annex crypto" ~: TestList $ flip map ["shared","hybrid","pubkey"] $
-    \scheme -> TestCase $ intmpclonerepo env $ whenM (Utility.Path.inPath Utility.Gpg.gpgcmd) $ do
-	Utility.Gpg.testTestHarness @? "test harness self-test failed"
-	Utility.Gpg.testHarness $ do
-		createDirectory "dir"
-		let a cmd = git_annex env cmd $
-			[ "foo"
-			, "type=directory"
-			, "encryption=" ++ scheme
-			, "directory=dir"
-			, "highRandomQuality=false"
-			] ++ if scheme `elem` ["hybrid","pubkey"]
-				then ["keyid=" ++ Utility.Gpg.testKeyId]
-				else []
-		a "initremote" @? "initremote failed"
-		not <$> a "initremote" @? "initremote failed to fail when run twice in a row"
-		a "enableremote" @? "enableremote failed"
-		a "enableremote" @? "enableremote failed when run twice in a row"
-		git_annex env "get" [annexedfile] @? "get of file failed"
-		annexed_present annexedfile
-		git_annex env "copy" [annexedfile, "--to", "foo"] @? "copy --to encrypted remote failed"
-		(c,k) <- annexeval $ do
-			uuid <- Remote.nameToUUID "foo"
-			rs <- Logs.Remote.readRemoteLog
-			Just (k,_) <- Backend.lookupFile annexedfile
-			return (fromJust $ M.lookup uuid rs, k)
-		let key = if scheme `elem` ["hybrid","pubkey"]
-				then Just $ Utility.Gpg.KeyIds [Utility.Gpg.testKeyId]
-				else Nothing
-		testEncryptedRemote scheme key c [k] @? "invalid crypto setup"
-
-		annexed_present annexedfile
-		git_annex env "drop" [annexedfile, "--numcopies=2"] @? "drop failed"
-		annexed_notpresent annexedfile
-		git_annex env "move" [annexedfile, "--from", "foo"] @? "move --from encrypted remote failed"
-		annexed_present annexedfile
-		not <$> git_annex env "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
-		annexed_present annexedfile
+test_crypto env = do
+	testscheme "shared"
+	testscheme "hybrid"
+	testscheme "pubkey"
   where
+	testscheme scheme = intmpclonerepo env $ whenM (Utility.Path.inPath Utility.Gpg.gpgcmd) $ do
+		Utility.Gpg.testTestHarness @? "test harness self-test failed"
+		Utility.Gpg.testHarness $ do
+			createDirectory "dir"
+			let a cmd = git_annex env cmd $
+				[ "foo"
+				, "type=directory"
+				, "encryption=" ++ scheme
+				, "directory=dir"
+				, "highRandomQuality=false"
+				] ++ if scheme `elem` ["hybrid","pubkey"]
+					then ["keyid=" ++ Utility.Gpg.testKeyId]
+					else []
+			a "initremote" @? "initremote failed"
+			not <$> a "initremote" @? "initremote failed to fail when run twice in a row"
+			a "enableremote" @? "enableremote failed"
+			a "enableremote" @? "enableremote failed when run twice in a row"
+			git_annex env "get" [annexedfile] @? "get of file failed"
+			annexed_present annexedfile
+			git_annex env "copy" [annexedfile, "--to", "foo"] @? "copy --to encrypted remote failed"
+			(c,k) <- annexeval $ do
+				uuid <- Remote.nameToUUID "foo"
+				rs <- Logs.Remote.readRemoteLog
+				Just (k,_) <- Backend.lookupFile annexedfile
+				return (fromJust $ M.lookup uuid rs, k)
+			let key = if scheme `elem` ["hybrid","pubkey"]
+					then Just $ Utility.Gpg.KeyIds [Utility.Gpg.testKeyId]
+					else Nothing
+			testEncryptedRemote scheme key c [k] @? "invalid crypto setup"
+	
+			annexed_present annexedfile
+			git_annex env "drop" [annexedfile, "--numcopies=2"] @? "drop failed"
+			annexed_notpresent annexedfile
+			git_annex env "move" [annexedfile, "--from", "foo"] @? "move --from encrypted remote failed"
+			annexed_present annexedfile
+			not <$> git_annex env "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
+			annexed_present annexedfile
 	{- Ensure the configuration complies with the encryption scheme, and
 	 - that all keys are encrypted properly for the given directory remote. -}
 	testEncryptedRemote scheme ks c keys = case Remote.Helper.Encryptable.extractCipher c of
@@ -974,7 +1016,7 @@ test_crypto env = "git-annex crypto" ~: TestList $ flip map ["shared","hybrid","
 		key2files cipher = Locations.keyPaths .
 			Crypto.encryptKey Types.Crypto.HmacSha1 cipher
 #else
-test_crypto _env = "git-annex crypto" ~: putStrLn "gpg testing not implemented on Windows"
+test_crypto _env = putStrLn "gpg testing not implemented on Windows"
 #endif
 
 -- This is equivilant to running git-annex, but it's all run in-process
diff --git a/Types/Distribution.hs b/Types/Distribution.hs
new file mode 100644
index 000000000..4201f49ad
--- /dev/null
+++ b/Types/Distribution.hs
@@ -0,0 +1,38 @@
+{- Data type for a distribution of git-annex
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Types.Distribution where
+
+import Types.Key
+import Data.Time.Clock
+import Git.Config (isTrue, boolConfig)
+
+data GitAnnexDistribution = GitAnnexDistribution
+	{ distributionUrl :: String
+	, distributionKey :: Key
+	, distributionVersion :: GitAnnexVersion
+	, distributionReleasedate :: UTCTime
+	, distributionUrgentUpgrade :: Maybe GitAnnexVersion
+	}
+	deriving (Read, Show, Eq)
+
+type GitAnnexVersion = String
+
+data AutoUpgrade = AskUpgrade | AutoUpgrade | NoAutoUpgrade
+	deriving (Eq)
+
+toAutoUpgrade :: (Maybe String) -> AutoUpgrade
+toAutoUpgrade Nothing = AskUpgrade
+toAutoUpgrade (Just s)
+	| s == "ask" = AskUpgrade
+	| isTrue s == Just True = AutoUpgrade
+	| otherwise = NoAutoUpgrade
+
+fromAutoUpgrade :: AutoUpgrade -> String
+fromAutoUpgrade AskUpgrade = "ask"
+fromAutoUpgrade AutoUpgrade = boolConfig True
+fromAutoUpgrade NoAutoUpgrade = boolConfig False
diff --git a/Types/GitConfig.hs b/Types/GitConfig.hs
index b573a9a25..7224f43ff 100644
--- a/Types/GitConfig.hs
+++ b/Types/GitConfig.hs
@@ -17,6 +17,7 @@ import qualified Git
 import qualified Git.Config
 import Utility.DataUnits
 import Config.Cost
+import Types.Distribution
 
 {- Main git-annex settings. Each setting corresponds to a git-config key
  - such as annex.foo -}
@@ -42,6 +43,7 @@ data GitConfig = GitConfig
 	, annexCrippledFileSystem :: Bool
 	, annexLargeFiles :: Maybe String
 	, annexFsckNudge :: Bool
+	, annexAutoUpgrade :: AutoUpgrade
 	, coreSymlinks :: Bool
 	, gcryptId :: Maybe String
 	}
@@ -70,6 +72,7 @@ extractGitConfig r = GitConfig
 	, annexCrippledFileSystem = getbool (annex "crippledfilesystem") False
 	, annexLargeFiles = getmaybe (annex "largefiles")
 	, annexFsckNudge = getbool (annex "fscknudge") True
+	, annexAutoUpgrade = toAutoUpgrade $ getmaybe (annex "autoupgrade")
 	, coreSymlinks = getbool "core.symlinks" True
 	, gcryptId = getmaybe "core.gcrypt-id"
 	}
diff --git a/Types/Key.hs b/Types/Key.hs
index f900ece2b..598d5ed20 100644
--- a/Types/Key.hs
+++ b/Types/Key.hs
@@ -60,7 +60,9 @@ key2file Key { keyBackendName = b, keySize = s, keyMtime = m, keyName = n } =
 	_ ?: _ = ""
 
 file2key :: FilePath -> Maybe Key
-file2key s = if key == Just stubKey || (keyName <$> key) == Just "" then Nothing else key
+file2key s
+	| key == Just stubKey || (keyName <$> key) == Just "" || (keyBackendName <$> key) == Just "" = Nothing
+	| otherwise = key
   where
 	key = startbackend stubKey s
 
@@ -91,6 +93,4 @@ prop_idempotent_key_encode :: Key -> Bool
 prop_idempotent_key_encode k = Just k == (file2key . key2file) k
 
 prop_idempotent_key_decode :: FilePath -> Bool
-prop_idempotent_key_decode f
-	| null f = True -- skip illegal empty filename
-	| otherwise = maybe True (\k -> key2file k == f) (file2key f)
+prop_idempotent_key_decode f = maybe True (\k -> key2file k == f) (file2key f)
diff --git a/Types/Remote.hs b/Types/Remote.hs
index 9afcbbe55..8a94dcc05 100644
--- a/Types/Remote.hs
+++ b/Types/Remote.hs
@@ -18,7 +18,7 @@ import Types.UUID
 import Types.GitConfig
 import Config.Cost
 import Utility.Metered
-import Git.Remote
+import Git.Types
 import Utility.SafeCommand
 
 type RemoteConfigKey = String
diff --git a/Upgrade.hs b/Upgrade.hs
index f0166bf8e..7385268e8 100644
--- a/Upgrade.hs
+++ b/Upgrade.hs
@@ -1,6 +1,6 @@
 {- git-annex upgrade support
  -
- - Copyright 2010 Joey Hess <joey@kitenet.net>
+ - Copyright 2010, 2013 Joey Hess <joey@kitenet.net>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -11,14 +11,40 @@ module Upgrade where
 
 import Common.Annex
 import Annex.Version
+import Config
 #ifndef mingw32_HOST_OS
 import qualified Upgrade.V0
 import qualified Upgrade.V1
 #endif
 import qualified Upgrade.V2
+import qualified Upgrade.V4
 
-upgrade :: Annex Bool
-upgrade = go =<< getVersion
+checkUpgrade :: Version -> Annex ()
+checkUpgrade = maybe noop error <=< needsUpgrade
+
+needsUpgrade :: Version -> Annex (Maybe String)
+needsUpgrade v
+	| v `elem` supportedVersions = ok
+	| v `elem` autoUpgradeableVersions = ifM (upgrade True)
+		( ok
+		, err "Automatic upgrade failed!"
+		)
+	| v `elem` upgradableVersions = err "Upgrade this repository: git-annex upgrade"
+	| otherwise = err "Upgrade git-annex."
+  where
+	err msg = return $ Just $ "Repository version " ++ v ++
+		" is not supported. " ++ msg
+	ok = return Nothing
+
+upgrade :: Bool -> Annex Bool
+upgrade automatic = do
+	upgraded <- go =<< getVersion
+	when upgraded $
+		ifM isDirect
+			( setVersion directModeVersion
+			, setVersion defaultVersion
+			)
+	return upgraded
   where
 #ifndef mingw32_HOST_OS
 	go (Just "0") = Upgrade.V0.upgrade
@@ -28,4 +54,5 @@ upgrade = go =<< getVersion
 	go (Just "1") = error "upgrade from v1 on Windows not supported"
 #endif
 	go (Just "2") = Upgrade.V2.upgrade
+	go (Just "4") = Upgrade.V4.upgrade automatic
 	go _ = return True
diff --git a/Upgrade/V4.hs b/Upgrade/V4.hs
new file mode 100644
index 000000000..147ace559
--- /dev/null
+++ b/Upgrade/V4.hs
@@ -0,0 +1,23 @@
+{- git-annex v4 -> v5 uppgrade support
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Upgrade.V4 where
+
+import Common.Annex
+import Config
+import Annex.Direct
+
+{- Direct mode only upgrade. -}
+upgrade :: Bool -> Annex Bool
+upgrade automatic = ifM isDirect
+	( do
+		unless automatic $
+			showAction "v4 to v5"
+		setDirect True
+		return True
+	, return False
+	)
diff --git a/Utility/Base64.hs b/Utility/Base64.hs
index ec660108a..0c6c8677a 100644
--- a/Utility/Base64.hs
+++ b/Utility/Base64.hs
@@ -7,7 +7,7 @@
 
 module Utility.Base64 (toB64, fromB64Maybe, fromB64) where
 
-import Codec.Binary.Base64
+import "dataenc" Codec.Binary.Base64
 import Data.Bits.Utils
 import Control.Applicative
 import Data.Maybe
diff --git a/Utility/Batch.hs b/Utility/Batch.hs
index 011d30c94..035a2eb04 100644
--- a/Utility/Batch.hs
+++ b/Utility/Batch.hs
@@ -10,7 +10,9 @@
 module Utility.Batch where
 
 import Common
+#ifndef mingw32_HOST_OS
 import qualified Build.SysConfig
+#endif
 
 #if defined(linux_HOST_OS) || defined(__ANDROID__)
 import Control.Concurrent.Async
diff --git a/Utility/DirWatcher.hs b/Utility/DirWatcher.hs
index d28381fae..5231286fc 100644
--- a/Utility/DirWatcher.hs
+++ b/Utility/DirWatcher.hs
@@ -1,10 +1,10 @@
 {- generic directory watching interface
  -
- - Uses inotify, or kqueue, or fsevents to watch a directory
+ - Uses inotify, or kqueue, or fsevents, or win32-notify to watch a directory
  - (and subdirectories) for changes, and runs hooks for different
  - sorts of events as they occur.
  -
- - Copyright 2012 Joey Hess <joey@kitenet.net>
+ - Copyright 2012-2013 Joey Hess <joey@kitenet.net>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -27,11 +27,15 @@ import Control.Concurrent
 import qualified Utility.FSEvents as FSEvents
 import qualified System.OSX.FSEvents as FSEvents
 #endif
+#if WITH_WIN32NOTIFY
+import qualified Utility.Win32Notify as Win32Notify
+import qualified System.Win32.Notify as Win32Notify
+#endif
 
 type Pruner = FilePath -> Bool
 
 canWatch :: Bool
-#if (WITH_INOTIFY || WITH_KQUEUE || WITH_FSEVENTS)
+#if (WITH_INOTIFY || WITH_KQUEUE || WITH_FSEVENTS || WITH_WIN32NOTIFY)
 canWatch = True
 #else
 #if defined linux_HOST_OS
@@ -47,7 +51,7 @@ canWatch = False
  - OTOH, with kqueue, often only one event is received, indicating the most
  - recent state of the file. -}
 eventsCoalesce :: Bool
-#if WITH_INOTIFY
+#if (WITH_INOTIFY || WITH_WIN32NOTIFY)
 eventsCoalesce = False
 #else
 #if (WITH_KQUEUE || WITH_FSEVENTS)
@@ -68,7 +72,7 @@ eventsCoalesce = undefined
  - still being written to, and then no add event will be received once the
  - writer closes it. -}
 closingTracked :: Bool
-#if (WITH_INOTIFY || WITH_FSEVENTS)
+#if (WITH_INOTIFY || WITH_FSEVENTS || WITH_WIN32NOTIFY)
 closingTracked = True
 #else
 #if WITH_KQUEUE
@@ -83,7 +87,7 @@ closingTracked = undefined
  - Fsevents generates events when an existing file is reopened and rewritten,
  - but not necessarily when it's opened once and modified repeatedly. -}
 modifyTracked :: Bool
-#if (WITH_INOTIFY || WITH_FSEVENTS)
+#if (WITH_INOTIFY || WITH_FSEVENTS || WITH_WIN32NOTIFY)
 modifyTracked = True
 #else
 #if WITH_KQUEUE
@@ -119,27 +123,35 @@ watchDir :: FilePath -> Pruner -> WatchHooks -> (IO FSEvents.EventStream -> IO F
 watchDir dir prune hooks runstartup =
 	runstartup $ FSEvents.watchDir dir prune hooks
 #else
+#if WITH_WIN32NOTIFY
+type DirWatcherHandle = Win32Notify.WatchManager
+watchDir :: FilePath -> Pruner -> WatchHooks -> (IO Win32Notify.WatchManager -> IO Win32Notify.WatchManager) -> IO DirWatcherHandle
+watchDir dir prune hooks runstartup =
+	runstartup $ Win32Notify.watchDir dir prune hooks
+#else
 type DirWatcherHandle = ()
 watchDir :: FilePath -> Pruner -> WatchHooks -> (IO () -> IO ()) -> IO DirWatcherHandle
 watchDir = undefined
 #endif
 #endif
 #endif
+#endif
 
-#if WITH_INOTIFY
 stopWatchDir :: DirWatcherHandle -> IO ()
+#if WITH_INOTIFY
 stopWatchDir = INotify.killINotify
 #else
 #if WITH_KQUEUE
-stopWatchDir :: DirWatcherHandle -> IO ()
 stopWatchDir = killThread
 #else
 #if WITH_FSEVENTS
-stopWatchDir :: DirWatcherHandle -> IO ()
 stopWatchDir = FSEvents.eventStreamDestroy
 #else
-stopWatchDir :: DirWatcherHandle -> IO ()
+#if WITH_WIN32NOTIFY
+stopWatchDir = Win32Notify.killWatchManager
+#else
 stopWatchDir = undefined
 #endif
 #endif
 #endif
+#endif
diff --git a/Utility/FileMode.hs b/Utility/FileMode.hs
index d76fb5703..46c6a31f5 100644
--- a/Utility/FileMode.hs
+++ b/Utility/FileMode.hs
@@ -64,13 +64,20 @@ preventWrite f = modifyFileMode f $ removeModes writeModes
 allowWrite :: FilePath -> IO ()
 allowWrite f = modifyFileMode f $ addModes [ownerWriteMode]
 
+{- Turns a file's owner read bit back on. -}
+allowRead :: FilePath -> IO ()
+allowRead f = modifyFileMode f $ addModes [ownerReadMode]
+
 {- Allows owner and group to read and write to a file. -}
-groupWriteRead :: FilePath -> IO ()
-groupWriteRead f = modifyFileMode f $ addModes
+groupSharedModes :: [FileMode]
+groupSharedModes =
 	[ ownerWriteMode, groupWriteMode
 	, ownerReadMode, groupReadMode
 	]
 
+groupWriteRead :: FilePath -> IO ()
+groupWriteRead f = modifyFileMode f $ addModes groupSharedModes
+
 checkMode :: FileMode -> FileMode -> Bool
 checkMode checkfor mode = checkfor `intersectFileModes` mode == checkfor
 
diff --git a/Utility/Misc.hs b/Utility/Misc.hs
index a2c9c8184..68199c828 100644
--- a/Utility/Misc.hs
+++ b/Utility/Misc.hs
@@ -15,11 +15,15 @@ import Foreign
 import Data.Char
 import Data.List
 import Control.Applicative
+import System.Exit
 #ifndef mingw32_HOST_OS
 import System.Posix.Process (getAnyProcessStatus)
 import Utility.Exception
 #endif
 
+import Utility.FileSystemEncoding
+import Utility.Monad
+
 {- A version of hgetContents that is not lazy. Ensures file is 
  - all read before it gets closed. -}
 hGetContentsStrict :: Handle -> IO String
@@ -29,6 +33,13 @@ hGetContentsStrict = hGetContents >=> \s -> length s `seq` return s
 readFileStrict :: FilePath -> IO String
 readFileStrict = readFile >=> \s -> length s `seq` return s
 
+{-  Reads a file strictly, and using the FileSystemEncofing, so it will
+ -  never crash on a badly encoded file. -}
+readFileStrictAnyEncoding :: FilePath -> IO String
+readFileStrictAnyEncoding f = withFile f ReadMode $ \h -> do
+	fileEncoding h
+	hClose h `after` hGetContentsStrict h
+
 {- Like break, but the item matching the condition is not included
  - in the second result list.
  -
@@ -136,3 +147,7 @@ reapZombies = do
 #else
 reapZombies = return ()
 #endif
+
+exitBool :: Bool -> IO a
+exitBool False = exitFailure
+exitBool True = exitSuccess
diff --git a/Utility/Process.hs b/Utility/Process.hs
index 53b6d2f2f..398e8a352 100644
--- a/Utility/Process.hs
+++ b/Utility/Process.hs
@@ -44,8 +44,10 @@ import qualified Control.Exception as E
 import Control.Monad
 #ifndef mingw32_HOST_OS
 import System.Posix.IO
-import Data.Maybe
+#else
+import Control.Applicative
 #endif
+import Data.Maybe
 
 import Utility.Misc
 import Utility.Exception
@@ -161,6 +163,8 @@ createBackgroundProcess p a = a =<< createProcess p
  - whether it succeeded or failed. -}
 processTranscript :: String -> [String] -> (Maybe String) -> IO (String, Bool)
 #ifndef mingw32_HOST_OS
+{- This implementation interleves stdout and stderr in exactly the order
+ - the process writes them. -}
 processTranscript cmd opts input = do
 	(readf, writef) <- createPipe
 	readh <- fdToHandle readf
@@ -173,10 +177,7 @@ processTranscript cmd opts input = do
 			}
 	hClose writeh
 
-	-- fork off a thread to start consuming the output
-	transcript <- hGetContents readh
-	outMVar <- newEmptyMVar
-	_ <- forkIO $ E.evaluate (length transcript) >> putMVar outMVar ()
+	get <- mkreader readh
 
 	-- now write and flush any input
 	case input of
@@ -188,15 +189,46 @@ processTranscript cmd opts input = do
 			hClose inh
 		Nothing -> return ()
 
-	-- wait on the output
-	takeMVar outMVar
-	hClose readh
+	transcript <- get
 
 	ok <- checkSuccessProcess pid
 	return (transcript, ok)
 #else
-processTranscript = error "processTranscript TODO"
+{- This implementation for Windows puts stderr after stdout. -}
+processTranscript cmd opts input = do
+	p@(_, _, _, pid) <- createProcess $
+		(proc cmd opts)
+			{ std_in = if isJust input then CreatePipe else Inherit
+			, std_out = CreatePipe
+			, std_err = CreatePipe
+			}
+
+	getout <- mkreader (stdoutHandle p)
+	geterr <- mkreader (stderrHandle p)
+
+	case input of
+		Just s -> do
+			let inh = stdinHandle p
+			unless (null s) $ do
+				hPutStr inh s
+				hFlush inh
+			hClose inh
+		Nothing -> return ()
+	
+	transcript <- (++) <$> getout <*> geterr
+	ok <- checkSuccessProcess pid
+	return (transcript, ok)
 #endif
+  where
+	mkreader h = do
+		s <- hGetContents h
+		v <- newEmptyMVar
+		void $ forkIO $ do
+			void $ E.evaluate (length s)
+			putMVar v ()
+		return $ do
+			takeMVar v
+			return s
 
 {- Runs a CreateProcessRunner, on a CreateProcess structure, that
  - is adjusted to pipe only from/to a single StdHandle, and passes
diff --git a/Utility/Quvi.hs b/Utility/Quvi.hs
index 5df1a4da7..4039167ac 100644
--- a/Utility/Quvi.hs
+++ b/Utility/Quvi.hs
@@ -11,9 +11,13 @@ module Utility.Quvi where
 
 import Common
 import Utility.Url
+import Build.SysConfig (newquvi)
 
 import Data.Aeson
 import Data.ByteString.Lazy.UTF8 (fromString)
+import qualified Data.Map as M
+import Network.URI (uriAuthority, uriRegName)
+import Data.Char
 
 data Page = Page
 	{ pageTitle :: String
@@ -25,6 +29,7 @@ data Link = Link
 	, linkUrl :: URLString
 	} deriving (Show)
 
+{- JSON instances for quvi 0.4. -}
 instance FromJSON Page where
 	parseJSON (Object v) = Page
 		<$> v .: "page_title"
@@ -37,6 +42,20 @@ instance FromJSON Link where
 		<*> v .: "url"
 	parseJSON _ = mzero
 
+{- "enum" format used by quvi 0.9 -}
+parseEnum :: String -> Maybe Page
+parseEnum s = Page
+	<$> get "QUVI_MEDIA_PROPERTY_TITLE"
+	<*> ((:[]) <$>
+		( Link
+			<$> get "QUVI_MEDIA_STREAM_PROPERTY_CONTAINER"
+			<*> get "QUVI_MEDIA_STREAM_PROPERTY_URL"
+		)
+	    )
+  where
+	get = flip M.lookup m
+	m = M.fromList $ map (separate (== '=')) $ lines s
+
 type Query a = [CommandParam] -> URLString -> IO a
 
 {- Throws an error when quvi is not installed. -}
@@ -54,8 +73,11 @@ query :: Query (Maybe Page)
 query ps url = flip catchNonAsync (const $ return Nothing) (query' ps url)
 
 query' :: Query (Maybe Page)
-query' ps url = decode . fromString
-	<$> readProcess "quvi" (toCommand $ ps ++ [Param url])
+query' ps url
+	| newquvi = parseEnum
+		<$> readProcess "quvi" (toCommand $ [Param "dump", Param "-p", Param "enum"] ++ ps ++ [Param url])
+	| otherwise = decode . fromString
+		<$> readProcess "quvi" (toCommand $ ps ++ [Param url])
 
 queryLinks :: Query [URLString]
 queryLinks ps url = maybe [] (map linkUrl . pageLinks) <$> query ps url
@@ -65,17 +87,47 @@ queryLinks ps url = maybe [] (map linkUrl . pageLinks) <$> query ps url
 check :: Query Bool
 check ps url = maybe False (not . null . pageLinks) <$> query ps url
 
-{- Checks if an url is supported by quvi, without hitting it, or outputting
+{- Checks if an url is supported by quvi, as quickly as possible
+ - (without hitting it if possible), and without outputting
  - anything. Also returns False if quvi is not installed. -}
 supported :: URLString -> IO Bool
-supported url = boolSystem "quvi" [Params "-v mute --support", Param url]
-
+supported url
+	{- Use quvi-info to see if the url's domain is supported.
+	 - If so, have to do a online verification of the url. -}
+	| newquvi = (firstlevel <&&> secondlevel)
+		`catchNonAsync` (\_ -> return False)
+	| otherwise = boolSystem "quvi" [Params "--verbosity mute --support", Param url]
+  where
+  	firstlevel = case uriAuthority =<< parseURIRelaxed url of
+		Nothing -> return False
+		Just auth -> do
+			let domain = map toLower $ uriRegName auth
+			let basedomain = intercalate "." $ reverse $ take 2 $ reverse $ split "." domain
+			any (\h -> domain `isSuffixOf` h || basedomain `isSuffixOf` h) 
+				. map (map toLower) <$> listdomains
+	secondlevel = snd <$> processTranscript "quvi"
+		(toCommand [Param "dump", Param "-o", Param url]) Nothing
+
+listdomains :: IO [String]
+listdomains 
+	| newquvi = concatMap (split ",") 
+		. concatMap (drop 1 . words) 
+		. filter ("domains: " `isPrefixOf`) . lines
+		<$> readProcess "quvi"
+			(toCommand [Param "info", Param "-p", Param "domains"])
+	| otherwise = return []
+
+{- Disables progress, but not information output. -}
 quiet :: CommandParam
-quiet = Params "-v quiet"
-
-noredir :: CommandParam
-noredir = Params "-e -resolve"
+quiet
+	-- Cannot use quiet as it now disables informational output.
+	-- No way to disable progress.
+	| newquvi = Params "--verbosity verbose"
+	| otherwise = Params "--verbosity quiet"
 
 {- Only return http results, not streaming protocols. -}
 httponly :: CommandParam
-httponly = Params "-c http"
+httponly
+	-- No way to do it with 0.9?
+	| newquvi = Params ""
+	| otherwise = Params "-c http"
diff --git a/Utility/Url.hs b/Utility/Url.hs
index 97296c920..03c311fd2 100644
--- a/Utility/Url.hs
+++ b/Utility/Url.hs
@@ -14,7 +14,8 @@ module Utility.Url (
 	checkBoth,
 	exists,
 	download,
-	downloadQuiet
+	downloadQuiet,
+	parseURIRelaxed
 ) where
 
 import Common
diff --git a/Utility/Win32Notify.hs b/Utility/Win32Notify.hs
new file mode 100644
index 000000000..edde5309c
--- /dev/null
+++ b/Utility/Win32Notify.hs
@@ -0,0 +1,65 @@
+{- Win32-notify interface
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Utility.Win32Notify where
+
+import Common hiding (isDirectory)
+import Utility.DirWatcher.Types
+
+import System.Win32.Notify
+import qualified System.PosixCompat.Files as Files
+
+watchDir :: FilePath -> (FilePath -> Bool) -> WatchHooks -> IO WatchManager
+watchDir dir ignored hooks = do
+	scan dir
+	wm <- initWatchManager
+	void $ watchDirectory wm dir True [Create, Delete, Modify, Move] handle
+	return wm
+  where
+	handle evt
+		| ignoredPath ignored (filePath evt) = noop
+		| otherwise = case evt of
+			(Deleted _ _)
+				| isDirectory evt -> runhook delDirHook Nothing
+				| otherwise -> runhook delHook Nothing
+			(Created _ _)
+				| isDirectory evt -> noop
+				| otherwise -> runhook addHook Nothing
+			(Modified _ _)
+				| isDirectory evt -> noop
+				{- Add hooks are run when a file is modified for 
+				 - compatability with INotify, which calls the add
+				 - hook when a file is closed, and so tends to call
+				 - both add and modify for file modifications. -}
+				| otherwise -> do
+					runhook addHook Nothing
+					runhook modifyHook Nothing
+	  where
+		runhook h s = maybe noop (\a -> a (filePath evt) s) (h hooks)
+
+	scan d = unless (ignoredPath ignored d) $
+		mapM_ go =<< dirContentsRecursive d
+	  where		
+		go f
+			| ignoredPath ignored f = noop
+			| otherwise = do
+				ms <- getstatus f
+				case ms of
+					Nothing -> noop
+					Just s
+						| Files.isRegularFile s ->
+							runhook addHook ms
+						| otherwise ->
+							noop
+		  where
+			runhook h s = maybe noop (\a -> a f s) (h hooks)
+		
+	getstatus = catchMaybeIO . getFileStatus
+
+{- Check each component of the path to see if it's ignored. -}
+ignoredPath :: (FilePath -> Bool) -> FilePath -> Bool
+ignoredPath ignored = any ignored . map dropTrailingPathSeparator . splitPath
diff --git a/debian/changelog b/debian/changelog
index 193976ac9..0a84e9307 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,110 @@
+git-annex (5.20131127) unstable; urgency=low
+
+  * webapp: Detect when upgrades are available, and upgrade if the user
+    desires.
+    (Only when git-annex is installed using the prebuilt binaries
+    from git-annex upstream, not from eg Debian.)
+  * assistant: Detect when the git-annex binary is modified or replaced,
+    and either prompt the user to restart the program, or automatically
+    restart it.
+  * annex.autoupgrade configures both the above upgrade behaviors.
+  * Added support for quvi 0.9. Slightly suboptimal due to limitations in its
+    interface compared with the old version.
+  * Bug fix: annex.version did not get set on automatic upgrade to v5 direct
+    mode repo, so the upgrade was performed repeatedly, slowing commands down.
+  * webapp: Fix bug that broke switching between local repositories
+    that use the new guarded direct mode.
+  * Android: Fix stripping of the git-annex binary.
+  * Android: Make terminal app show git-annex version number.
+  * Android: Re-enable XMPP support.
+  * reinject: Allow to be used in direct mode.
+  * Futher improvements to git repo repair. Has now been tested in tens
+    of thousands of intentionally damaged repos, and successfully
+    repaired them all.
+  * Allow use of --unused in bare repository.
+
+ -- Joey Hess <joeyh@debian.org>  Wed, 27 Nov 2013 18:41:44 -0400
+
+git-annex (5.20131120) unstable; urgency=low
+
+  * Fix Debian package to not try to run test suite, since haskell-tasty
+    is not out of new or in Build-Depends yet.
+  * dropunused, addunused: Allow "all" instead of a range to
+    act on all unused data.
+  * Ensure execute bit is set on directories when core.sharedrepository is set.
+  * Ensure that core.sharedrepository is honored when creating the .git/annex
+    directory.
+  * Improve repair code in the case where the index file is corrupt,
+    and this hides other problems from git fsck.
+
+ -- Joey Hess <joeyh@debian.org>  Wed, 20 Nov 2013 12:54:18 -0400
+
+git-annex (5.20131118) unstable; urgency=low
+
+  * Direct mode repositories now have core.bare=true set, to prevent
+    accidentally running git commands that try to operate on the work tree,
+    and so do the wrong thing in direct mode.
+  * annex.version is now set to 5 for direct mode repositories.
+    This upgrade is handled fully automatically, no need to run
+    git annex upgrade
+  * The "status" command has been renamed to "info", to allow
+    "git annex status" to be used in direct mode repositories, now that
+    "git status" won't work in them.
+  * The -c option now not only modifies the git configuration seen by
+    git-annex, but it is passed along to every git command git-annex runs.
+  * watcher: Avoid loop when adding a file owned by someone else fails
+    in indirect mode because its permissions cannot be modified.
+  * webapp: Avoid encoding problems when displaying the daemon log file.
+  * webapp: Improve UI around remote that have no annex.uuid set,
+    either because setup of them is incomplete, or because the remote
+    git repository is not a git-annex repository.
+  * Include ssh-keygen in standalone bundle.
+  * Allow optionally configuring git-annex with -fEKG to enable awesome
+    remote monitoring interfaceat http://localhost:4242/
+  * Fix bug that caused bad information to be written to the git-annex branch
+    when running describe or other commands with a remote that has no uuid.
+  * Work around Android linker problem that had prevented git-annex from
+    running on Android 4.3 and 4.4.
+  * repair: Handle case where index file is corrupt, but all objects are ok.
+  * assistant: Notice on startup when the index file is corrupt, and
+    auto-repair.
+  * Fix direct mode merge bug when a direct mode file was deleted and replaced
+    with a directory. An ordering problem caused the directory to not get
+    created in this case.
+    Thanks to Tim for the test case.
+  * Direct mode .git/annex/objects directories are no longer left writable,
+    because that allowed writing to symlinks of files that are not present,
+    which followed the link and put bad content in an object location.
+    Thanks to Tim for the test case.
+  * fsck: Fix up .git/annex/object directory permissions.
+  * Switched to the tasty test framework.
+  * Android: Adjust default .gitignore to ignore .thumbnails at any location
+    in the tree, not just at its top.
+  * webapp: Check annex.version.
+
+ -- Joey Hess <joeyh@debian.org>  Mon, 18 Nov 2013 10:45:43 -0400
+
+git-annex (4.20131106) unstable; urgency=low
+
+  * Improve local pairing behavior when two computers both try to start
+    the pairing process separately.
+  * sync: Work even when the local git repository is new and empty,
+    with no master branch.
+  * gcrypt, bup: Fix bug that prevented using these special remotes
+    with encryption=pubkey.
+  * Fix enabling of gcrypt repository accessed over ssh;
+    git-annex-shell gcryptsetup had a bug that caused it to fail
+    with permission denied.
+  * Fix zombie process that occurred when switching between repository
+    views in the webapp.
+  * map: Work when there are gcrypt remotes.
+  * Fix build w/o webapp.
+  * Fix exception handling bug that could cause .git/annex/index to be used
+    for git commits outside the git-annex branch. Known to affect git-annex
+    when used with the git shipped with Ubuntu 13.10.
+
+ -- Joey Hess <joeyh@debian.org>  Wed, 06 Nov 2013 11:17:47 -0400
+
 git-annex (4.20131101) unstable; urgency=low
 
   * The "git annex content" command is renamed to "git annex wanted".
diff --git a/debian/control b/debian/control
index 911974604..6fbd2a06a 100644
--- a/debian/control
+++ b/debian/control
@@ -53,7 +53,7 @@ Build-Depends:
 	libghc-feed-dev,
 	ikiwiki,
 	perlmagick,
-	git,
+	git (>= 1:1.8.4),
 	rsync,
 	wget,
 	curl,
@@ -68,7 +68,7 @@ Package: git-annex
 Architecture: any
 Section: utils
 Depends: ${misc:Depends}, ${shlibs:Depends},
-	git (>= 1:1.7.7.6),
+	git (>= 1:1.8.4),
 	rsync,
 	wget,
 	curl,
diff --git a/debian/rules b/debian/rules
index 3a0511fa6..91854aa15 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,9 @@ export RELEASE_BUILD=1
 %:
 	dh $@
 
+override_dh_auto_test:
+	echo test suite currently disabled until haskell-tasty is out of NEW
+
 # Not intended for use by anyone except the author.
 announcedir:
 	@echo ${HOME}/src/git-annex/doc/news
diff --git a/doc/assistant/downloadupgrade.png b/doc/assistant/downloadupgrade.png
new file mode 100644
index 000000000..157eaddc7
--- /dev/null
+++ b/doc/assistant/downloadupgrade.png
diff --git a/doc/assistant/remote_sharing_walkthrough/comment_4_978fab3cd165b4ca245e32fc48cf0970._comment b/doc/assistant/remote_sharing_walkthrough/comment_4_978fab3cd165b4ca245e32fc48cf0970._comment
new file mode 100644
index 000000000..ab0b19160
--- /dev/null
+++ b/doc/assistant/remote_sharing_walkthrough/comment_4_978fab3cd165b4ca245e32fc48cf0970._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 4"
+ date="2013-11-12T18:18:16Z"
+ content="""
+You can easily use a removable drive as a transfer repository to sync two computers that have no network connection. Just use the webapp to add the drive on one computer. The drive will be set up as a transfer repository by default. The webapp will automatically start copying all your files to it. Then you can disconnect the drive, bring it to the other computer, and repeat the process. Everything from the first computer will then sync over from the drive to the second computer. And repeat moving the drive back and forth to keep things in sync.
+"""]]
diff --git a/doc/assistant/remote_sharing_walkthrough/comment_4_d7e879f7b098964040df2e27a18eda72._comment b/doc/assistant/remote_sharing_walkthrough/comment_4_d7e879f7b098964040df2e27a18eda72._comment
new file mode 100644
index 000000000..71f57e9b3
--- /dev/null
+++ b/doc/assistant/remote_sharing_walkthrough/comment_4_d7e879f7b098964040df2e27a18eda72._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="Using a portable drive as another transfer device?"
+ date="2013-11-12T16:52:12Z"
+ content="""
+I try to understand how to setup git-annex for the following use case:
+
+Two computers, that are paired via remote sharing, using some cloud repository for transfer, and a local NAS for backups.
+
+These two computers are sometimes in the same network, sometimes in different networks, and sometimes even without network at all. From what I read, it should be possible to bypass the cloud when these two machines are on the same network, which sounds great.
+
+Would it be possible to use a portable drive as \"another link\" between these two computers that can be used to sync them even if there is no network between them?
+
+And as you write, if the pairing has been set up manually, then everything is fine - so could it be that it is really easy and only necessary to setup the git-annex on the local drive as an additional remote on both (or only one?) machine?
+
+thanks for any insight!
+"""]]
diff --git a/doc/assistant/remote_sharing_walkthrough/comment_5_00852736d47c05772b15c5ff54ae7da7._comment b/doc/assistant/remote_sharing_walkthrough/comment_5_00852736d47c05772b15c5ff54ae7da7._comment
new file mode 100644
index 000000000..a66fcd098
--- /dev/null
+++ b/doc/assistant/remote_sharing_walkthrough/comment_5_00852736d47c05772b15c5ff54ae7da7._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="Using a portable drive as another transfer device? – cool."
+ date="2013-11-14T19:05:56Z"
+ content="""
+Thanks - I was hoping that it is that easy. I'll try that as soon as I have a working version of the latest git-annex (trying to build with brew for Mac OS X 10.9, but without success so far). 
+"""]]
diff --git a/doc/assistant/upgradecomplete.png b/doc/assistant/upgradecomplete.png
new file mode 100644
index 000000000..3f8c7f3c2
--- /dev/null
+++ b/doc/assistant/upgradecomplete.png
diff --git a/doc/bare_repositories.mdwn b/doc/bare_repositories.mdwn
index 7fa035985..975a638b8 100644
--- a/doc/bare_repositories.mdwn
+++ b/doc/bare_repositories.mdwn
@@ -39,7 +39,7 @@ Now configure the remote and do the initial push:
     git remote add origin example.com:bare-annex.git
     git push origin master git-annex
 
-Now `git annex status` should show the configured bare remote. If it does not, you may have to pull from the remote first (older versions of `git-annex`)
+Now `git annex info` should show the configured bare remote. If it does not, you may have to pull from the remote first (older versions of `git-annex`)
 
 If you wish to configure git such that you can push/pull without arguments, set the upstream branch:
 
diff --git a/doc/bugs/127.0.0.1_references_on_remote_assistant_access.mdwn b/doc/bugs/127.0.0.1_references_on_remote_assistant_access.mdwn
new file mode 100644
index 000000000..bf62df8d5
--- /dev/null
+++ b/doc/bugs/127.0.0.1_references_on_remote_assistant_access.mdwn
@@ -0,0 +1,20 @@
+### Please describe the problem.
+When I use git-annex webapp with a remote IP of a headless computer, I am sometimes redirected to a 127.0.0.1 address (with a different port as well)
+
+### What steps will reproduce the problem?
+1. Install git-annex as usual. 
+2. Open git-annex assistant from a headless machine and access the webapp with the --listen option. (e.g. git annex webapp --listen=xxx.yyy.zzz.www)
+3. Create your first local repository. Then create a second local repository.
+4. When assistant asks you if you want to merge these 2 repositories, try to select the second option (to keep them separated).
+5. You are redirected from your remote IP to 127.0.0.1 to a new port number.
+
+(I also encountered the same error at another menu or function, but I don't remember where. Sorry.) 
+
+### What version of git-annex are you using? On what operating system?
+4.20130815
+Ubuntu 13.10 64-bit (kernel 3.11.0-13-generic x86_64)
+
+### Please provide any additional information below.
+Please ask me for any additional information that may be useful.
+
+> [[dup]] of [[Hangs_on_creating_repository_when_using_--listen]]; [[done]] --[[Joey]]
diff --git a/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing.mdwn b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing.mdwn
new file mode 100644
index 000000000..a13bb95e3
--- /dev/null
+++ b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing.mdwn
@@ -0,0 +1,21 @@
+### Please describe the problem.
+
+I expected at least a listing of files... ideally with basic navigation and options to select/deselect to be fetched/dropped
+
+### What steps will reproduce the problem?
+
+Click on "Files" link near "Repository: " on top right of the Dashboard
+
+### What version of git-annex are you using? On what operating system?
+
+last Android build from Nov 18 2013
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
diff --git a/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_1_a9b03d4f4760fea2754a4dc93547f0a3._comment b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_1_a9b03d4f4760fea2754a4dc93547f0a3._comment
new file mode 100644
index 000000000..69cfaefd2
--- /dev/null
+++ b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_1_a9b03d4f4760fea2754a4dc93547f0a3._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T16:12:42Z"
+ content="""
+git-annex does not have a built-in file manager. I don't know how to get android to display a file manager; if there's a command that can be run, or an intent that can be used to get one, git-annex could do that. But I don't think android typically includes a file manager, I have only seen them as OEM addons on some of the more laptop form factor android devices.
+
+I think that the android web browser also does not support browsing file:// uri, which is what git-annex falls back to when it cannot file a file manager to top. 
+"""]]
diff --git a/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_2_015e859a16b1ce4c0c7601df0594d555._comment b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_2_015e859a16b1ce4c0c7601df0594d555._comment
new file mode 100644
index 000000000..039acd440
--- /dev/null
+++ b/doc/bugs/Android:_Clocking_on___34__Files__34___in_the_Dashboard_seems_to_do_nothing/comment_2_015e859a16b1ce4c0c7601df0594d555._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://yarikoptic.myopenid.com/"
+ nickname="site-myopenid"
+ subject="comment 2"
+ date="2013-11-27T04:36:14Z"
+ content="""
+Thanks for the explanation!  Might be better then to remove Files in Android build to prevent confusion?
+
+OI filemanager http://www.openintents.org/en/filemanager  I believe is open source.  according to app info it is only 1.53MB (thus negligible in comparison) and probably could be 'collaborated with' so they could ship basic support for annex (git annex get/drop)... I just don't know if it would be possible to start existing OI manager under annex user (that would be needed right?).
+"""]]
diff --git a/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__.mdwn b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__.mdwn
new file mode 100644
index 000000000..08b44fc93
--- /dev/null
+++ b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__.mdwn
@@ -0,0 +1,24 @@
+### Please describe the problem.
+
+Upon a new (re-)installation of Android ("proper" build as from http://downloads.kitenet.net/git-annex/android/current/4.0/git-annex.apk  Last-Modified: Mon, 18 Nov 2013 11:57:25 GMT), as well as whatever was day before a daily build, I am getting a message in web ui "not supported  This build of git-annex does not support XMPP pairing. Sorry!" whenever I am entering "Share with your other devices" among "Add more repositories".
+
+### What steps will reproduce the problem?
+
+I had some older and then freshier (yesterday daily build) installed.  Then uninstalled and current "proper" build installed.
+it picked up initialized repository I did yesterday but when I went into "Share ..." link  I saw the message without any option to add such another device
+
+### What version of git-annex are you using? On what operating system?
+
+Android
+
+About says   5.20131118-gc7e5cde.  
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
diff --git a/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_1_c034bb84e58b2dda1038ba205ec78c56._comment b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_1_c034bb84e58b2dda1038ba205ec78c56._comment
new file mode 100644
index 000000000..ef0661cb8
--- /dev/null
+++ b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_1_c034bb84e58b2dda1038ba205ec78c56._comment
@@ -0,0 +1,273 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T17:23:52Z"
+ content="""
+I think that older Android builds did support this (IIRC). However, I recently rebootstrapped my android dev environment, and when I enable the XMPP flag now:
+
+<pre>
+system.c:222:0:  error: undefined reference to 'pthread_atfork'
+
+cipher.c:213:0:  error: undefined reference to 'nettle_cbc_encrypt'
+
+cipher.c:213:0:  error: undefined reference to 'nettle_cbc_decrypt'
+
+cipher.c:213:0:  error: undefined reference to 'nettle_des_encrypt'
+
+cipher.c:213:0:  error: undefined reference to 'nettle_des_decrypt'
+
+cipher.c:213:0:
+     error: undefined reference to 'nettle_arcfour_crypt'
+
+cipher.c:213:0:
+     error: undefined reference to 'nettle_des3_encrypt'
+
+cipher.c:213:0:
+     error: undefined reference to 'nettle_des3_decrypt'
+
+cipher.c:213:0:
+     error: undefined reference to 'nettle_arctwo_encrypt'
+
+cipher.c:213:0:
+     error: undefined reference to 'nettle_arctwo_decrypt'
+
+cipher.c:265:0:
+     error: undefined reference to 'nettle_arcfour_set_key'
+
+cipher.c:68:0:
+     error: undefined reference to 'nettle_aes_set_encrypt_key'
+
+cipher.c:69:0:
+     error: undefined reference to 'nettle_aes_invert_key'
+
+cipher.c:96:0:
+     error: undefined reference to 'nettle_camellia_set_encrypt_key'
+
+cipher.c:97:0:
+     error: undefined reference to 'nettle_camellia_invert_key'
+
+cipher.c:268:0:
+     error: undefined reference to 'nettle_arctwo_set_key'
+
+cipher.c:239:0:
+     error: undefined reference to 'nettle_des_fix_parity'
+
+cipher.c:242:0:
+     error: undefined reference to 'nettle_des3_set_key'
+
+cipher.c:255:0:
+     error: undefined reference to 'nettle_des_fix_parity'
+
+cipher.c:257:0:  error: undefined reference to 'nettle_des_set_key'
+
+cipher.c:83:0:  error: undefined reference to 'nettle_aes_decrypt'
+
+cipher.c:76:0:  error: undefined reference to 'nettle_aes_encrypt'
+
+cipher.c:111:0:
+     error: undefined reference to 'nettle_camellia_crypt'
+
+cipher.c:104:0:
+     error: undefined reference to 'nettle_camellia_crypt'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha256_update'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha224_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha224_set_key'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_md5_update'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_md5_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_md5_set_key'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha1_update'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha1_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha1_set_key'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha256_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha256_set_key'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha512_update'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha384_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha384_set_key'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha512_digest'
+
+mac.c:146:0:
+     error: undefined reference to 'nettle_hmac_sha512_set_key'
+
+mac.c:243:0:  error: undefined reference to 'nettle_sha224_init'
+
+mac.c:222:0:  error: undefined reference to 'nettle_md5_init'
+
+mac.c:229:0:  error: undefined reference to 'nettle_sha1_init'
+
+mac.c:236:0:  error: undefined reference to 'nettle_md2_init'
+
+mac.c:250:0:  error: undefined reference to 'nettle_sha256_init'
+
+mac.c:257:0:  error: undefined reference to 'nettle_sha384_init'
+
+mac.c:264:0:  error: undefined reference to 'nettle_sha512_init'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha256_update'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha224_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_md5_update'
+
+mac.c:278:0:  error: undefined reference to 'nettle_md5_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha1_update'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha1_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_md2_update'
+
+mac.c:278:0:  error: undefined reference to 'nettle_md2_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha256_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha512_update'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha384_digest'
+
+mac.c:278:0:  error: undefined reference to 'nettle_sha512_digest'
+
+mpi.c:48:0:
+     error: undefined reference to 'nettle_mpz_sizeinbase_256_u'
+
+mpi.c:80:0:  error: undefined reference to 'nettle_mpz_get_str_256'
+
+mpi.c:76:0:  error: undefined reference to 'nettle_mpz_get_str_256'
+
+mpi.c:52:0:
+     error: undefined reference to 'nettle_mpz_sizeinbase_256_s'
+
+mpi.c:56:0:
+     error: undefined reference to 'nettle_mpz_sizeinbase_256_u'
+
+mpi.c:142:0:
+     error: undefined reference to 'nettle_mpz_set_str_256_u'
+
+mpi.c:117:0:
+     error: undefined reference to 'nettle_mpz_set_str_256_u'
+
+mpi.c:121:0:
+     error: undefined reference to 'nettle_mpz_set_str_256_s'
+
+mpi.c:470:0:
+     error: undefined reference to 'nettle_mpz_set_str_256_u'
+
+mpi.c:496:0:
+     error: undefined reference to 'nettle_mpz_set_str_256_u'
+
+pk.c:505:0:
+     error: undefined reference to 'nettle_dsa_public_key_init'
+
+pk.c:506:0:
+     error: undefined reference to 'nettle_dsa_private_key_init'
+
+pk.c:515:0:
+     error: undefined reference to 'nettle_dsa_generate_keypair'
+
+pk.c:545:0:
+     error: undefined reference to 'nettle_dsa_private_key_clear'
+
+pk.c:546:0:
+     error: undefined reference to 'nettle_dsa_public_key_clear'
+
+pk.c:558:0:
+     error: undefined reference to 'nettle_rsa_public_key_init'
+
+pk.c:559:0:
+     error: undefined reference to 'nettle_rsa_private_key_init'
+
+pk.c:563:0:
+     error: undefined reference to 'nettle_rsa_generate_keypair'
+
+pk.c:598:0:
+     error: undefined reference to 'nettle_rsa_private_key_clear'
+
+pk.c:599:0:
+     error: undefined reference to 'nettle_rsa_public_key_clear'
+
+pk.c:598:0:
+     error: undefined reference to 'nettle_rsa_private_key_clear'
+
+pk.c:599:0:
+     error: undefined reference to 'nettle_rsa_public_key_clear'
+
+pk.c:545:0:
+     error: undefined reference to 'nettle_dsa_private_key_clear'
+
+pk.c:546:0:
+     error: undefined reference to 'nettle_dsa_public_key_clear'
+
+pk.c:286:0:
+     error: undefined reference to 'nettle_dsa_signature_init'
+
+pk.c:296:0:  error: undefined reference to '_nettle_dsa_sign'
+
+pk.c:309:0:
+     error: undefined reference to 'nettle_dsa_signature_clear'
+
+pk.c:344:0:
+     error: undefined reference to 'nettle_rsa_compute_root'
+
+pk.c:309:0:
+     error: undefined reference to 'nettle_dsa_signature_clear'
+
+pk.c:231:0:
+     error: undefined reference to 'nettle_rsa_compute_root'
+
+pk.c:441:0:  error: undefined reference to '_nettle_dsa_verify'
+
+rnd.c:222:0:
+     error: undefined reference to 'nettle_yarrow256_update'
+
+rnd.c:340:0:
+     error: undefined reference to 'nettle_yarrow256_update'
+
+rnd.c:284:0:
+     error: undefined reference to 'nettle_yarrow256_update'
+
+rnd.c:388:0:
+     error: undefined reference to 'nettle_yarrow256_slow_reseed'
+
+rnd.c:465:0:
+     error: undefined reference to 'nettle_yarrow256_random'
+
+rnd.c:421:0:  error: undefined reference to 'nettle_yarrow256_init'
+
+rnd.c:437:0:
+     error: undefined reference to 'nettle_yarrow256_slow_reseed'
+collect2: error: ld returned 1 exit status
+make: *** [android] Error 1
+</pre>
+
+
+"""]]
diff --git a/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_2_99a754f41d59fdd401ba6d169945e7c9._comment b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_2_99a754f41d59fdd401ba6d169945e7c9._comment
new file mode 100644
index 000000000..6c5f48d5c
--- /dev/null
+++ b/doc/bugs/Android___34__This_build_of_git-annex_does_not_support_XMPP_pairing__34__/comment_2_99a754f41d59fdd401ba6d169945e7c9._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 2"
+ date="2013-11-26T19:40:55Z"
+ content="""
+Managed to get it to build with XMPP, but it was quite a hack job getting the C libraries to behave, and I have not been able to test it yet. The daily build has it if you want to give it a try.
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories.mdwn b/doc/bugs/Assistant_has_created_155_semitrusted_repositories.mdwn
new file mode 100644
index 000000000..b1caf530d
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories.mdwn
@@ -0,0 +1,191 @@
+### Please describe the problem.
+git annex status reports 160 semitrusted repositories. Four of them are the ones I created (only via webapp, I think I never edited any git-annex config file). One is 	00000000-0000-0000-0000-000000000001 -- web
+ and although I do not know what it is, it is not something new. The remaining 155 appeared spontaneously after several Gb of data (mostly many small files) were added to an Annex (in an 'archive' directory) operated in direct mode by the assistant.
+
+
+
+### What steps will reproduce the problem?
+Add several Gb of files was enough to trigger this problem, but I did not try to reproduce it. It happened the day I installed the 4.20131106~bpo70+1 version.
+
+### What version of git-annex are you using? On what operating system?
+
+4.20131106~bpo70+1 on debian squeeze (7.2), with git  1.8.4.rc3.
+
+
+### Please provide any additional information below.
+May be related or not: at some point the webapp displayed two warning boxes. One of them held a message that I did not wirte down and proposed to "Restart the thread". This apparently worked since the box disappeared. The other warning box indicated "NetWatcherFallback crashed: unknown response from git cat-file" and proposed to restart the thread. Trying to "restart the thread" via the provided button just did not trigger any response of the webapp which seemed dead at that point.
+
+In spite of the git annex status shown below, the webapp still shows only the expected four repositories.
+
+Output of git annex status (hostname and xmpp account name were edited away):
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+repository mode: direct
+trusted repositories: 
+0
+semitrusted repositories: 160
+	00000000-0000-0000-0000-000000000001 -- web
+ 	0ab193eb-0c76-4559-a93c-2e30ed8630a8 -- someMachineIown_datadir (archive)
+ 	1384784127.91222s -- 1 391b0557-dc68-4e40-b6d0-da3033588753
+ 	1384784164.437824s -- 1 391b0557-dc68-4e40-b6d0-da3033588753
+ 	1384784176.944372s -- 1 391b0557-dc68-4e40-b6d0-da3033588753
+ 	1384784179.254498s -- 1 391b0557-dc68-4e40-b6d0-da3033588753
+ 	1384785147.558938s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384785147.717223s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384785159.041203s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384785159.199504s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384785185.79485s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384785187.318128s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
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+ 	1384969784.725195s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384969786.49773s -- 0 391b0557-dc68-4e40-b6d0-da3033588753
+ 	1384969814.984624s -- 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+ 	1384969815.397676s -- 0 391b0557-dc68-4e40-b6d0-da3033588753
+ 	391b0557-dc68-4e40-b6d0-da3033588753 -- here (client)
+ 	668ef9d8-68c6-484e-89e5-06634d590a11 -- rsync.net_datadir_annex (transfer)
+ 	b0d3c000-0ac9-4a05-aef4-47f826d5c759 -- user.name (client)
+
+
+# End of transcript or log.
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_1_169b24b34cce3f5c8446c2150beb6827._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_1_169b24b34cce3f5c8446c2150beb6827._comment
new file mode 100644
index 000000000..99bb737e4
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_1_169b24b34cce3f5c8446c2150beb6827._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-22T16:54:53Z"
+ content="""
+Please post the output of `git show git-annex:uuid.log` run in the repository.
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_2_6acd6f38297772a07d8d5fb999bd2eaa._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_2_6acd6f38297772a07d8d5fb999bd2eaa._comment
new file mode 100644
index 000000000..6db2a8fca
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_2_6acd6f38297772a07d8d5fb999bd2eaa._comment
@@ -0,0 +1,183 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnNqLKszWk9EoD4CDCqNXJRIklKFBCN1Ao"
+ nickname="maurizio"
+ subject="comment 2"
+ date="2013-11-22T17:23:19Z"
+ content="""
+Here it is (user name edited):
+
+[[!format sh \"\"\"
+
+
+0ab193eb-0c76-4559-a93c-2e30ed8630a8 archive timestamp=1384664310.014349s
+0ab193eb-0c76-4559-a93c-2e30ed8630a8 datadir on st08 timestamp=1384522780.868451s
+0ab193eb-0c76-4559-a93c-2e30ed8630a8 username@st08:~/datadir_annex timestamp=1384540428.076617s
+0ab193eb-0c76-4559-a93c-2e30ed8630a8 username@st08:~/datadir_annex timestamp=1384541057.852874s
+0ab193eb-0c76-4559-a93c-2e30ed8630a8 username@st08:~/datadir_annex timestamp=1384548609.891111s
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+391b0557-dc68-4e40-b6d0-da3033588753 client timestamp=1384528843.958836s
+391b0557-dc68-4e40-b6d0-da3033588753 username@big:~/datadir/Annex timestamp=1384521164.194035s
+668ef9d8-68c6-484e-89e5-06634d590a11 cipher=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 encryption=shared name=rsync.net_datadir_annex rsyncurl=rsusername@git-annex-ch-s011.rsync.net-rsusername_datadir_annex.2F:datadir_annex/ type=rsync timestamp=1384948273.302009s
+668ef9d8-68c6-484e-89e5-06634d590a11 cipher=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 encryption=shared name=rsync.net_datadir_annex rsyncurl=rsusername@git-annex-ch-s011.rsync.net-rsusername_datadir_annex:datadir_annex/ type=rsync timestamp=1384547300.727425s
+668ef9d8-68c6-484e-89e5-06634d590a11 rsync.net_datadir_annex timestamp=1384547300.725734s
+668ef9d8-68c6-484e-89e5-06634d590a11 rsync.net_datadir_annex timestamp=1384948273.280063s
+668ef9d8-68c6-484e-89e5-06634d590a11 transfer timestamp=1384948273.352386s
+b0d3c000-0ac9-4a05-aef4-47f826d5c759 client timestamp=1384575989.965159s
+b0d3c000-0ac9-4a05-aef4-47f826d5c759 username@mezzo:~/datadir/Annex timestamp=1384547220.353298s
+
+\"\"\"]]
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_3_6a4118e5c5fbe5e84d27094ac72b741b._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_3_6a4118e5c5fbe5e84d27094ac72b741b._comment
new file mode 100644
index 000000000..2d31d1a7a
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_3_6a4118e5c5fbe5e84d27094ac72b741b._comment
@@ -0,0 +1,22 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 3"
+ date="2013-11-22T17:47:30Z"
+ content="""
+Any chance I could get a copy of this git repository? (Excluding the .git/annex part)
+
+Feel free to email me id@joeyh.name to arrange a secure transfer.
+
+Otherwise, I need to see what the git-annex:uuid.log file looked like before this happened to it. The corruption may have occurred progressively in several commits, or all at once.
+
+You might also still have some logs in `.git/annex/daemon.log*`, and sending those might help, assuming the strange messages you mentioned are logged in there.
+
+> 1384785215.389096s 1 0ab193eb-0c76-4559-a93c-2e30ed8630a8
+
+This is pretty weird thing to be in the uuid.log. The \"1\" makes me think this might be a scrambled version of what's normally stored in the trust.log:
+
+> 511f4722-63d5-11e1-8b26-1bb951ea9f7b 1 timestamp=1330630786.417597s
+
+This seems to be the same bug as [[bugs/non-repos in repositories list (+ other weird output) from git annex status]]
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_4_04daa20d5d7c74bb34ec48e752ed9fe8._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_4_04daa20d5d7c74bb34ec48e752ed9fe8._comment
new file mode 100644
index 000000000..dd037bcc0
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_4_04daa20d5d7c74bb34ec48e752ed9fe8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 4"
+ date="2013-11-22T17:48:37Z"
+ content="""
+What hardware are you running git-annex on?
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_5_11af8ab2587e6eeb671051ba8191995b._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_5_11af8ab2587e6eeb671051ba8191995b._comment
new file mode 100644
index 000000000..de9d4fd71
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_5_11af8ab2587e6eeb671051ba8191995b._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnNqLKszWk9EoD4CDCqNXJRIklKFBCN1Ao"
+ nickname="maurizio"
+ subject="comment 5"
+ date="2013-11-22T18:22:55Z"
+ content="""
+One client is a thinkpad 121e, the other one a hp Z420 workstation. The archive is a basic Dell desktop. All of them run wheezy with git-annex and git  from official backports. The transfer repository is at rsync.net. 
+
+The daemon.log file was empty at the time I noticed the situation. Now git-annex has been scanning this repository for some time and the log has information again but it looks a bit too long to be posted here. I will email about the repository copy and the log.
+
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_6_26236cdc2bce532017854791bcd727d1._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_6_26236cdc2bce532017854791bcd727d1._comment
new file mode 100644
index 000000000..8b5c80f6b
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_6_26236cdc2bce532017854791bcd727d1._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnNqLKszWk9EoD4CDCqNXJRIklKFBCN1Ao"
+ nickname="maurizio"
+ subject="comment 6"
+ date="2013-11-22T19:29:08Z"
+ content="""
+Some additional information (useful at least from user's point of view): the data that was in the annex but outside of the archive is still accessible from both clients. Part of the data that was in the archive does not seem to be accessible on one client: ```git annex get```  says it gets data in an amount which seems correct but the link to the data remains broken. Fortunately I can still access the data on the other client. Some of the data in the archive is still accessible in both clients. The part that is still accessible was put in the annex a few days ago, only the last directory which was added and seems to have triggered the problem is \"broken\" on one client. It is possible (not sure, sorry) that this directory was first added in the annex, and then moved to the archive shortly after, before the first addition had propagated to the other client.
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_7_3c532dd5b8a01ecdeda1300b49aba675._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_7_3c532dd5b8a01ecdeda1300b49aba675._comment
new file mode 100644
index 000000000..00abc500b
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_7_3c532dd5b8a01ecdeda1300b49aba675._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnNqLKszWk9EoD4CDCqNXJRIklKFBCN1Ao"
+ nickname="maurizio"
+ subject="comment 7"
+ date="2013-11-23T13:16:10Z"
+ content="""
+OK, sorry but it will be difficult to provide you with a copy of this repository. I hope I can still help in spite of being only a very novice git user. I checked that the git-annex:uuid.log file at the first commit was identical to the one above.  The only difference is that in this first commit file there is a mention at the bottom of who created the file (me@somedomain.com) with the mention \"created repository\". 
+
+So it is very possible that these nonexisting remotes are present since day 1. It is possible that I did not notice it earlier (I am not sure I had ever run git annex status in this repository since I am looking for a dropbox-like experience). What triggered my curiosity was the difficulty I had to get some data. At that point it might be that there are two independent problems. One with these nonexisting repositories, and another one with the fact that I cannot get some data in this client.
+
+Would it be useful to you to have the full history (52 revisions) of the git-annex:uuid.log file?
+"""]]
diff --git a/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_8_119142c5ebc499f0ee0926dbca265308._comment b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_8_119142c5ebc499f0ee0926dbca265308._comment
new file mode 100644
index 000000000..d50964f64
--- /dev/null
+++ b/doc/bugs/Assistant_has_created_155_semitrusted_repositories/comment_8_119142c5ebc499f0ee0926dbca265308._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 8"
+ date="2013-11-26T16:34:13Z"
+ content="""
+Yes, it would be helpful to have the full history of the file.
+
+You might try running `git annex fsck` on the file in the client that it says it has gotten but that you cannot access.
+"""]]
diff --git a/doc/bugs/Assistant_redirects_to_127.0.0.1_in_some_cases__44___although_used_remotely.mdwn b/doc/bugs/Assistant_redirects_to_127.0.0.1_in_some_cases__44___although_used_remotely.mdwn
new file mode 100644
index 000000000..1b1738aec
--- /dev/null
+++ b/doc/bugs/Assistant_redirects_to_127.0.0.1_in_some_cases__44___although_used_remotely.mdwn
@@ -0,0 +1,29 @@
+### Please describe the problem.
+When I use git-annex webapp with a remote IP of a headless computer,
+I am sometimes redirected to a 127.0.0.1 address (with a different
+port as well)
+
+### What steps will reproduce the problem?
+1. Install git-annex as usual.
+2. Open git-annex assistant from a headless machine and access the
+webapp with the --listen option. (e.g. git annex webapp
+--listen=xxx.yyy.zzz.www)
+3. Create your first local repository. Then create a second local
+repository.
+4. When assistant asks you if you want to merge these 2
+repositories, try to select the second option (to keep them
+separated).
+5. You are redirected from your remote IP to 127.0.0.1 to a new port number.
+
+(I also encountered the same error at another menu or function, but
+I don't remember where. Sorry.)
+
+### What version of git-annex are you using? On what operating system?
+4.20130815
+Ubuntu 13.10 64-bit (kernel 3.11.0-13-generic x86_64)
+
+### Please provide any additional information below.
+Please ask me for any additional information that may be useful.
+
+> This is a duplicate of [[Switching_repositories_in_webapp_on_a_remote_server_is_not_honoring_--listen_parameter]]
+> [[done]] --[[Joey]] 
diff --git a/doc/bugs/Assistant_uses_obsolete_GDU_volume_monitor/comment_3_d86aba42d014c4b4f708dcb5fe86e055._comment b/doc/bugs/Assistant_uses_obsolete_GDU_volume_monitor/comment_3_d86aba42d014c4b4f708dcb5fe86e055._comment
index c1bc52f2c..6256086c7 100644
--- a/doc/bugs/Assistant_uses_obsolete_GDU_volume_monitor/comment_3_d86aba42d014c4b4f708dcb5fe86e055._comment
+++ b/doc/bugs/Assistant_uses_obsolete_GDU_volume_monitor/comment_3_d86aba42d014c4b4f708dcb5fe86e055._comment
@@ -6,5 +6,5 @@
  content="""
 I've just committed support for using the new name. I've not been able to test it yet, as I don't have a new enough gnome here. Any testing you can do much appreciated.
 
-Leaving this bug open until it gets tested, and also because it's certianly appealing to just use poll rather than this fragile dbus stuff. And in any case, should add OSX support.
+Leaving this bug open until it gets tested, and also because it's certainly appealing to just use poll rather than this fragile dbus stuff. And in any case, should add OSX support.
 """]]
diff --git a/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_5_118d61dea9ef0faa2960da6f2f62ec8b._comment b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_5_118d61dea9ef0faa2960da6f2f62ec8b._comment
new file mode 100644
index 000000000..28299c372
--- /dev/null
+++ b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_5_118d61dea9ef0faa2960da6f2f62ec8b._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://id.koumbit.net/anarcat"
+ ip="2001:1928:1:9::1"
+ subject="sources"
+ date="2013-11-21T18:41:12Z"
+ content="""
+I tried to find a canonical source for why (or if?) git ignores any \".git\" directory, and it turns out it also ignores .git *files*, according to [this stackoverflow thread](http://stackoverflow.com/questions/6839781/what-happens-when-you-run-git-add-git-in-a-git-repository). It's hardcoded in the source code and \"will likely not change\".
+
+I guess this should therefore be taken upstream, but I am not sure how this could justified there.
+
+I do think git-annex should support that. It's turning more and more as a \"generic backup solution\" or \"i want my files in the cloud\" kind of solution, which is awesome, but small things like this are making it harder to use... --[[anarcat]]
+"""]]
diff --git a/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_6_3978557c6e85608243e5b4eb698ac5a5._comment b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_6_3978557c6e85608243e5b4eb698ac5a5._comment
new file mode 100644
index 000000000..da52be691
--- /dev/null
+++ b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_6_3978557c6e85608243e5b4eb698ac5a5._comment
@@ -0,0 +1,27 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkkyBDsfOB7JZvPZ4a8F3rwv0wk6Nb9n48"
+ nickname="Abdó"
+ subject="comment 6"
+ date="2013-11-21T20:04:22Z"
+ content="""
+After I wrote my last post in this thread I did write a patch for git doing two things:
+
+* make git ignore .git only at the root of the working tree, but not '.git' files or directories nested deeper into the working tree. 
+* add config option to prevent git from converting directories containing .git into gitlinks. It turns out that git already has an internal setting for this, it only needed to be exposed in the config files!
+
+It kind of worked, but I've never used nor completed this, though (if I recall correctly, something had to be done regarding the default gitingores, which contains .git). I don't think upstream would accept these changes, though. It is a potentially risky change that does not gives them any benefit. Plus commiting a git repo inside an other is kind of crazy. I'm not convinced this is a good solution anymore.
+
+Being able to put a git repo inside an assistant-controled directory would be nice, though. Additionally, letting the outermost git repo recognize the internal git repo as a git repo, instead of moving files blindly, would also be nice, and probably more reasonable. And that leads to submodules...
+
+My particular problem is: I want to syncing a directory with lots of little git repos across several machines, without having to configure remotes for every single one of them (so no mr) and having someone take care of the files which are ignored by the little git repos, possibly as annexed files. Currently I just sync that folder containing the little git repos with unison.
+
+Now, instead of commiting git repos inside git repos, I'm more inclined to a potential solution using git-annex + submodules. Ideally I'd like something like this:
+
+1. A git-annex repo at ~/work
+2. All my little git repos inside ~/work are automatically recognized as submodules by git-annex
+3. The outermost git-annex takes care of the .gitignored files for the inner git repos
+4. git pull/push --recursive on the outermost annex repo pulls/pushes submodules (I think [something like this](https://github.com/jlehmann/git-submod-enhancements/wiki/Recursive-submodule-checkout) is written by  Jens Lehmann)
+5. The urls in .gitmodules are relative paths from the outermost annex working tree. Then a git fetch --recursive from the outermost annex can use an outermost remote + the submodule relative path. No need to manually configure remotes for every machine on every submodule!
+
+The problem with this approach, is that 2,4,5 are science-fiction for now, and probably 3 too. Realizing this would imply a lot of work, and commiting a lot of submodule stuff to upstream git. But probably stuff that makes sense and they would accept. Anyway, I'd like to know what Joey thinks about all this...
+"""]]
diff --git a/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_7_e6dfc41d2042402b40efb6f6139d5662._comment b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_7_e6dfc41d2042402b40efb6f6139d5662._comment
new file mode 100644
index 000000000..374d193c0
--- /dev/null
+++ b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_7_e6dfc41d2042402b40efb6f6139d5662._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 7"
+ date="2013-11-22T16:50:31Z"
+ content="""
+I appreciate the investigation.
+
+Now that there's a direct mode guard, it would be possible to have git-annex translate .git directories to some other name when adding files to git. This seems more likely than getting git changed.
+
+However, I am not convinced *at all* that it makes any sense to try to sync git repositories in this way. I realize that some people drop git checkouts into dropbox and use that, but it's a fundamentally unsound thing to do, and those people are just lucky if they manage to avoid running into problems doing that.
+
+If you have two clones of a repo, and a git repository is checked into both, and they become partitioned for a while and larger re-merge, then there can be conflicts in the files that make up the git repository. Which git-annex would auto-resolve, with the effect that the checked-in git repository would appear to be broken.
+
+Also, this feature would only be used by a small number of users, on the border between people who can use git the Correct Way, and people who don't use git other than with the assistant.
+
+It would make sense to make git-annex refuse to add files inside nested git repositories though.
+"""]]
diff --git a/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_8_33a84937c87dd2406bc090a0d2969683._comment b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_8_33a84937c87dd2406bc090a0d2969683._comment
new file mode 100644
index 000000000..df97625f7
--- /dev/null
+++ b/doc/bugs/Can__39__t_add_a_git_repo_to_git_annex:___34__Invalid_path_repo__47__.git__47__X__34___for_many_X/comment_8_33a84937c87dd2406bc090a0d2969683._comment
@@ -0,0 +1,30 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkkyBDsfOB7JZvPZ4a8F3rwv0wk6Nb9n48"
+ nickname="Abdó"
+ subject="comment 8"
+ date="2013-11-22T18:44:35Z"
+ content="""
+> I am not convinced at all that it makes any sense to try to sync git repositories in this way
+
+I agree this is not a good solution.
+
+
+> I realize that some people drop git checkouts into dropbox and use that, but it's a fundamentally unsound thing to do, and those people are just lucky if they manage to avoid running into problems doing that.
+
+Well, I don't use dropbox (nor annex assistant) but I sync a lot of git repos with unison. It is not luck, it is being careful not to create conflicts. I agree this is not ideal, and I'm looking for a better way to deal with this.
+
+
+> Also, this feature would only be used by a small number of users
+
+I'm not convinced of that. If done right, nested git repos inside annex could have value.
+
+Let's say you work with 40 git repos some private of yours, others tracking upstream, and you want to sync them across 4 machines (home, work, cloud server, backup). I imagine your preferred solution would be to configure the 4 machines as remotes on every git repo and use mr, am I right?
+
+This has its problems:
+
+1. The set of files you want in the project git repo may not be the same as the set of files you want synced across machines. For instance, I use a large software project that I compile from sources. I want to sync binaries across machines (it takes forever to compile!), but of course I don't want them commited into the project, not even as annexed files.
+2. Configuring remotes for every project is tedious. What if some remote changes url? what if I want to change the path of some of the git projects? Every time I add a new repo I need to configure all the 4 remotes. This can be scripted of course, but is not my ideal solution.
+
+What do you think about the submodules route I proposed? I don't like submodules very much, but in this case, I think it could become a good solution. In particular it would solve 1, 2 above and be able to merge conflicting changes on the nested repos.
+
+"""]]
diff --git a/doc/bugs/Conflicting_archive_descriptions.mdwn b/doc/bugs/Conflicting_archive_descriptions.mdwn
new file mode 100644
index 000000000..832daa4ea
--- /dev/null
+++ b/doc/bugs/Conflicting_archive_descriptions.mdwn
@@ -0,0 +1,16 @@
+This is confusing:
+
+"Next we come to the archive repositories.The archive repositories coordinate together, so that each file is archived in only one place. **When you move files into a folder named "archive"**, they'll be moved to an archive repository, and removed from all your client repositories. This is handy if you have old files you don't need anymore, but want to keep archived for later. When you copy or move a file out of an "archive" folder, it'll be retrieved from the archive repository."
+
+"The small archive repositories are like other archive repositories, but smaller. While archive repositories normally accumulate every file they can, small archive repositories only accumulate files **once you put them in an "archive" directory.**"
+
+Based upon those descriptions, I don't know what the difference is.
+
+> Improved wording to not imply that files are only put into archive
+> repositories once the files are moved to archive directories.
+> (Which is how small archive repositories work.)
+> 
+> If you're still confused about it, see
+> <http://git-annex.branchable.com/assistant/archival_walkthrough/>
+> 
+> [[done]] --[[Joey]]
diff --git a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_3_a9f202a1d3eb652b83bc54e6b017084a._comment b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_3_a9f202a1d3eb652b83bc54e6b017084a._comment
deleted file mode 100644
index 7359f2f80..000000000
--- a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_3_a9f202a1d3eb652b83bc54e6b017084a._comment
+++ /dev/null
@@ -1,12 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
- nickname="Carlo"
- subject="comment 3"
- date="2013-10-30T15:04:44Z"
- content="""
-The assistant autorecovered my work repo before I noticed, so it looks like I can't provide the necessary info. There were a bunch of files missing that got re-synced from my home PC.
-
-For what it's worth, I noticed that on my phone, when cutting the internet connection while syncing, the assistant downloaded existing files into placeholder files, and then continued actually downloading files when they were around.
-
-
-"""]]
diff --git a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_4_d5fc95f8909d3fd7786afef451558053._comment b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_4_d5fc95f8909d3fd7786afef451558053._comment
deleted file mode 100644
index 4d8e9f598..000000000
--- a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_4_d5fc95f8909d3fd7786afef451558053._comment
+++ /dev/null
@@ -1,12 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
- nickname="Carlo"
- subject="comment 4"
- date="2013-10-30T15:05:17Z"
- content="""
-The assistant autorecovered my work repo before I noticed, so it looks like I can't provide the necessary info. There were a bunch of files missing that got re-synced from my home PC.
-
-For what it's worth, I noticed that on my phone, when cutting the internet connection while syncing, the assistant downloaded existing files into placeholder files, and then continued actually downloading files when the network connection was restored.
-
-
-"""]]
diff --git a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_5_6058a22b733cb02126286af950074ed4._comment b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_5_6058a22b733cb02126286af950074ed4._comment
new file mode 100644
index 000000000..33e85c772
--- /dev/null
+++ b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_5_6058a22b733cb02126286af950074ed4._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 5"
+ date="2013-11-03T01:17:39Z"
+ content="""
+I don't understand what you mean by \"The assistant autorecovered my work repo before I noticed\". What repo is the work repo, and how could the assistant \"autorecover\" it, and what did it do?
+
+At this point, I am completely in the dark about whether you're reporting a problem, and what the problem is. 
+"""]]
diff --git a/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_6_5a348c5f327f16e1192ef6bd7f2880bb._comment b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_6_5a348c5f327f16e1192ef6bd7f2880bb._comment
new file mode 100644
index 000000000..7e611cebd
--- /dev/null
+++ b/doc/bugs/Corrupted_drive:_Assistant_seems_consider_files_deleted_and_deletes_them_elsewhere_too/comment_6_5a348c5f327f16e1192ef6bd7f2880bb._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
+ nickname="Carlo"
+ subject="comment 6"
+ date="2013-11-19T09:48:26Z"
+ content="""
+Sorry, missed the comment.
+
+My work repo is the repository on my work laptop, where deletions got synced to.
+
+Git annex had then run repository repair automatically, so the odd symlinks where no longer there for me to check out.
+
+It is possible that I ran some git commands in direct mode I shouldn't have; I put the files back in and it's working nicely now. So this might have been a \"no direct mode guard\" issue.
+
+"""]]
diff --git a/doc/bugs/Discrepancy_between_git_annex_add_and_git_annex_watch.mdwn b/doc/bugs/Discrepancy_between_git_annex_add_and_git_annex_watch.mdwn
new file mode 100644
index 000000000..8e836e345
--- /dev/null
+++ b/doc/bugs/Discrepancy_between_git_annex_add_and_git_annex_watch.mdwn
@@ -0,0 +1,33 @@
+### Please describe the problem.
+
+`git annex add` does not add dotfiles (as per the man page) while `git annex watch` does (nothing on the man page). It's not a bug, but rather a surprise (at least to me).
+
+### What steps will reproduce the problem?
+
+[[!format sh """
+git init dotfiles
+cd dotfiles
+git annex init "my dotfiles"
+echo test > test.txt
+echo dottest > .dotest.txt
+git annex add
+git commit -a -m "initial dots"
+git annex whereis .dotest.txt # no answer, as expected
+git annex watch
+git annex whereis .dotest.txt # answers that .dotest.txt is here
+"""]]
+
+### What version of git-annex are you using? On what operating system?
+git-annex version: 4.20131101, ubuntu 12.04 with all updates.
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
+
+> Improved documentation. [[done]] --[[Joey]]
diff --git a/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder.mdwn b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder.mdwn
index 5d60b64da..d011e4416 100644
--- a/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder.mdwn
+++ b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder.mdwn
@@ -3743,3 +3743,5 @@ To repoB:/media/srv/img/
 (Recording state in git...)
 # End of transcript or log.
 """]]
+
+> [[done]], seems this was caused by the bug I alread fixed. --[[Joey]]
diff --git a/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_3_650dc9ede4e16ef668d96840f63dad47._comment b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_3_650dc9ede4e16ef668d96840f63dad47._comment
new file mode 100644
index 000000000..4e7d6491c
--- /dev/null
+++ b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_3_650dc9ede4e16ef668d96840f63dad47._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T20:03:33Z"
+ content="""
+I don't understand why there are so many commits that need to be reverted. I'd have thought that it would have only made one bad commit due to the bug, and reverting that would do. Or even just adding back any symlinks removed by any of the bad commits, without an explicit revert would accomplish the same.
+
+You should be able to check with `git annex whereis --not --in .` what git-annex thinks about the 200 broken symlinks. Clearly their content is not in the local repisitory; it may be present elsewhere, or you might have to restore those files from backup.
+
+Once you have the git tree of the repository back in good shape, assuming you did it by committing changes, and possibly committing git reverts, you should be able to just use normal git annex syncing to sync those changes to the second repo. Ie, `git annex sync` in both, or running the assistant.
+"""]]
diff --git a/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_4_721cf184fb5a5244ec5c15de3302ebf7._comment b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_4_721cf184fb5a5244ec5c15de3302ebf7._comment
new file mode 100644
index 000000000..3876444cd
--- /dev/null
+++ b/doc/bugs/During_synchronisation_top-level_folder_suddenly_appear_in_sub-sub-folder/comment_4_721cf184fb5a5244ec5c15de3302ebf7._comment
@@ -0,0 +1,33 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnh6wz0pMA3NLPFg2j_I3S5JeinaOVqnng"
+ nickname="Felix"
+ subject="Number of commits"
+ date="2013-11-21T20:26:46Z"
+ content="""
+I have no idea where this large number of commits come from, but maybe the sheer number of files explains it:
+
+Files appearing in the wrong place (probably due to me starting the assistant in a subdirectory of the repo):
+
+    $ git log --stat | grep \"5d/20.*+$\" |wc -l
+    1148
+
+Me wondering where they come from and deleting them manually step by step when I found them:
+
+    $ git log --stat | grep \"5d/20.*-$\" |wc -l
+    1095
+
+git-annex removing the original files that have been mirrored in the wrong place (and maybe a few more as I was working on stuff there as well):
+
+    $ git log --stat | grep \"^ 20.*-$\" | wc -l
+    1152
+
+Maybe this explains the large number (approx. 500) of commits?
+
+---
+
+The missing 200 files have not been in a different repo, so apart from 3 that were not available they have been restored from the backup.
+
+---
+
+As my setup needs some changes anyway I'm going to start from scratch. 
+"""]]
diff --git a/doc/bugs/Endless_SSH_password_prompts.mdwn b/doc/bugs/Endless_SSH_password_prompts.mdwn
new file mode 100644
index 000000000..26def613f
--- /dev/null
+++ b/doc/bugs/Endless_SSH_password_prompts.mdwn
@@ -0,0 +1,15 @@
+### Please describe the problem.
+Yesterday I installed git-annex on two computers and paired their repos.  Today I logged back in to one of them, and as soon as the webapp loaded (autostarted in the background), it popped up an OpenSSH prompt wanting my key's password.  I typed it in, and it popped up another.  This went on several times.  When I hit Cancel instead, it popped up a prompt wanting the password for the user account on my other computer.  Even with that, once wasn't enough.
+
+This is bad enough, but worse is that the password prompt captures the keyboard input so I can't even open my Yakuake console to kill git-annex.  Well, it's difficult and requires hitting Escape rapidly over and over until I can squeeze in a keystroke to the rest of the system.
+
+I don't understand why this is happening.
+
+1.  Shouldn't git-annex have installed a passwordless key on my paired system?  It did that for my remote repo.
+
+2.  The prompt it's using has no option to remember the pasword.  I use ssh-agent, but usually by running ssh-add in a terminal.  Maybe if it would use a prompt that works with the agent it wouldn't ask for the password multiple times.  
+
+3.  I think it's opening multiple SSH connections at once, before I've entered the password even once, so even after I enter the password, it will keep asking for it until I've entered it for every SSH process that was already started.
+
+### What version of git-annex are you using? On what operating system?
+1 Nov 2013 Linux tarball on Ubuntu Raring 13.04
diff --git a/doc/bugs/Endless_SSH_password_prompts/comment_1_b3a32d7a53c30478f409a47f856282ab._comment b/doc/bugs/Endless_SSH_password_prompts/comment_1_b3a32d7a53c30478f409a47f856282ab._comment
new file mode 100644
index 000000000..b1ea71526
--- /dev/null
+++ b/doc/bugs/Endless_SSH_password_prompts/comment_1_b3a32d7a53c30478f409a47f856282ab._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-03T00:29:14Z"
+ content="""
+Pairing sets up the same kind of dedicated passwordless ssh key that is used when adding a ssh server.
+
+It's not clear from your description what program is asking for the password, or even if it's asking for the password for a ssh key. You need to provide more details.
+"""]]
diff --git a/doc/bugs/Endless_SSH_password_prompts/comment_2_0a1fc4b4580d8be4c37064e0a16de99b._comment b/doc/bugs/Endless_SSH_password_prompts/comment_2_0a1fc4b4580d8be4c37064e0a16de99b._comment
new file mode 100644
index 000000000..fec729ddb
--- /dev/null
+++ b/doc/bugs/Endless_SSH_password_prompts/comment_2_0a1fc4b4580d8be4c37064e0a16de99b._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 2"
+ date="2013-11-03T00:39:38Z"
+ content="""
+I'm not sure which program is doing the asking either.  The title bar says \"OpenSSH\".  It is asking for the SSH key password, but if I dismiss the dialog without entering the password, it will open another dialog asking for the user account's password, e.g. me@laptop, indicating it's SSH falling back to password auth.
+"""]]
diff --git a/doc/bugs/Endless_SSH_password_prompts/comment_3_46210f7745b8c7c237fc8b08309390fe._comment b/doc/bugs/Endless_SSH_password_prompts/comment_3_46210f7745b8c7c237fc8b08309390fe._comment
new file mode 100644
index 000000000..aacf1cc01
--- /dev/null
+++ b/doc/bugs/Endless_SSH_password_prompts/comment_3_46210f7745b8c7c237fc8b08309390fe._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlHNJ7FpiXJNwSmojlwKwXhhF5QvwpNPmI"
+ nickname="Colin"
+ subject="Confirmed"
+ date="2013-11-14T17:57:23Z"
+ content="""
+I am seeing the same problem. It happened on a machine running git-annex on Debian Testing some weeks ago, and I eventually disabled the offending repository for my sanity (incidentally - it seems to have vanished so I don't know how to re-enable it apart from adding it again).
+
+It has just very recently (some days) started on this machine running Debian Unstable.
+
+"""]]
diff --git a/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_1_b524e70156e8bc1219d5c6741974ad99._comment b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_1_b524e70156e8bc1219d5c6741974ad99._comment
new file mode 100644
index 000000000..6b741e85e
--- /dev/null
+++ b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_1_b524e70156e8bc1219d5c6741974ad99._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlq4ClC5EMN1Vq1DpWXAqP5TiDnCK1mSfk"
+ nickname="Jonas"
+ subject="Happens with import, too"
+ date="2013-11-24T23:24:09Z"
+ content="""
+This happens to me when using git annex import, too (on version 4.20131106)
+
+    (Recording state in git...)
+    The following paths are ignored by one of your .gitignore files:
+    path/to/some/directory/.svn
+    Use -f if you really want to add them.
+    fatal: no files added
+
+    git-annex: user error (xargs [\"-0\",\"git\",\"--git-dir=/path/to/annex/.git\",\"--work-tree=/path/to/annex\",\"add\",\"--\"] exited 123)
+failed
+
+"""]]
diff --git a/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_2_ff7349c396d1249204d621e71f6a7a52._comment b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_2_ff7349c396d1249204d621e71f6a7a52._comment
new file mode 100644
index 000000000..2ee7f79b6
--- /dev/null
+++ b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_2_ff7349c396d1249204d621e71f6a7a52._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 2"
+ date="2013-11-26T20:04:23Z"
+ content="""
+This bug was fixed, and closed 2 years ago. Posting a comment about another, related problem is not very useful. 
+
+Yes, git annex import does not finish importing files if you've configured .gititnore to not allow those files to be added. If you need to do that, you could use `git annex import --force`, which will add the files despite the gitignore. 
+"""]]
diff --git a/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_4_4bc7d4c51faea3fdafc977cb66b7f73a._comment b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_4_4bc7d4c51faea3fdafc977cb66b7f73a._comment
new file mode 100644
index 000000000..a3a6fc10a
--- /dev/null
+++ b/doc/bugs/Error_when_moving_annexed_file_to_a_.gitignored_location/comment_4_4bc7d4c51faea3fdafc977cb66b7f73a._comment
@@ -0,0 +1,26 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlq4ClC5EMN1Vq1DpWXAqP5TiDnCK1mSfk"
+ nickname="Jonas"
+ subject="comment 4"
+ date="2013-11-27T17:36:39Z"
+ content="""
+Sorry, my bug triaging skills are limited. This one happened to have exactly the same error message...
+
+This might again be the wrong thread, but... how does git annex decide which files to ignore? In particular, it seems not always to agree with git:
+
+    $ cd /tmp
+    $ mkdir annex
+    $ cd annex
+    $ git init
+    $ git annex init \"Testing annex in /tmp\"
+    $ echo \"This file is hidden\" > .hidden_file
+    $ git status
+    shows .hidden_file as \"untracked\"
+    $ git annex add .
+    does nothing
+    $ git annex add --force .
+    does nothing, either
+    $ git add .
+    adds the file as expected
+
+"""]]
diff --git a/doc/bugs/Finding_an_Unused_file.mdwn b/doc/bugs/Finding_an_Unused_file.mdwn
index 211755829..c0e613163 100644
--- a/doc/bugs/Finding_an_Unused_file.mdwn
+++ b/doc/bugs/Finding_an_Unused_file.mdwn
@@ -146,7 +146,7 @@ upgrade supported from repository versions: 0 1 2
 """]]
 
 > If `git log -S` does not find the key, then it was not used for any
-> commit currently in the git repository. Which is certianly possible;
+> commit currently in the git repository. Which is certainly possible;
 > for example `git annex add file; git rm file`.
 > 
 > This is a dup of [[todo/wishlist: option to print more info with 'unused']]; [[done]] --[[Joey]] 
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn
new file mode 100644
index 000000000..d66196acd
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn
@@ -0,0 +1,44 @@
+### Please describe the problem.
+Using the webapp to generate a new (local) repository instantly takes it to the following state:
+[[!format sh """
+user@local:~/Annex$ git status
+# On branch master
+# Changes to be committed:
+#   (use "git reset HEAD <file>..." to unstage)
+#
+#	deleted:    uuid.log
+#
+user@local:~/Annex$ git branch
+  git-annex
+* master
+user@local:~/Annex$ git log
+commit 90bfcaf17b0576d8ecdc48ae44dda22d41464acc
+Author: local  <user>
+Date:   Sun Nov 3 15:30:17 2013 +0100
+
+    created repository
+user@local:~/Annex$ git show HEAD
+commit 90bfcaf17b0576d8ecdc48ae44dda22d41464acc
+Author: local  <user>
+Date:   Sun Nov 3 15:30:17 2013 +0100
+
+    created repository
+
+diff --git a/uuid.log b/uuid.log
+new file mode 100644
+index 0000000..9df3670
+--- /dev/null
++++ b/uuid.log
+@@ -0,0 +1 @@
++987e7b9a-aa9d-41db-ae92-23fcae7f6187 user@local:~/Annex timestamp=1383489017.181
+user@local:~/Annex$ 
+"""]]
+
+I'm new to git-annex, so I'm not quite sure, but looking at [[internals]] this file should only exist in the git-annex branch, not in master. Furthermore, from this state it seems impossible to get "sync with your other devices" to work, because of a merge conflict on this change.
+
+Perhaps some sort of a race-condition with the annex-assistant picking up the uuid.log file while the repository is being initialized?
+
+### What version of git-annex are you using? On what operating system?
+Ubuntu 13.10 with git-annex 4.20130815
+
+> [[fixed|done]]; see comments. (This fix needs to be backported to Ubuntu.) --[[Joey]] 
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_1_6441dd04adc158df22589c81746108a9._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_1_6441dd04adc158df22589c81746108a9._comment
new file mode 100644
index 000000000..6080e88e4
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_1_6441dd04adc158df22589c81746108a9._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-03T16:48:25Z"
+ content="""
+I can't reproduce this at all. What version of git do you have installed? Did you install git-annex from ubuntu's repository? Does the same thing happen if you install the standalone linux tarball and use it to make a new repository?
+
+git-annex never creates a file named uuid.log on disk, so it's quite strange that it shows up in the initial commit to the master branch. It sort of looks like somehow git-annex's normal use of a separate index file to stage the uuid.log to the git-annex branch is failing. Since I have never seen any problem with that, I have to suspect that the ubuntu build is somehow badly broken. Or that the git in Ubuntu is for some reason ignoring `GIT_INDEX_FILE`.
+"""]]
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_2_d1c5d7642284a375f9c455dbf76efa5c._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_2_d1c5d7642284a375f9c455dbf76efa5c._comment
new file mode 100644
index 000000000..50bff5f41
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_2_d1c5d7642284a375f9c455dbf76efa5c._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 2"
+ date="2013-11-03T17:02:47Z"
+ content="""
+I made an Ubuntu saucy chroot, apt-get installed git-annex from universe, and ran the webapp in there. I did not reproduce this problem. 
+
+The cause of the problem, it seems, must be something local to your system. Perhaps you have an environment variable set that is messing up git. Or perhaps you have a different, broken version of git installed.
+
+Can you \"git show git-annex\" in the repository? It should show a commit made to the git-annex branch that adds the uuid.log there.
+"""]]
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_3_4b863da1c8ba73ad54da20f7d2ec6e5c._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_3_4b863da1c8ba73ad54da20f7d2ec6e5c._comment
new file mode 100644
index 000000000..7acab1c37
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_3_4b863da1c8ba73ad54da20f7d2ec6e5c._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="tanen"
+ ip="83.128.159.25"
+ subject="comment 3"
+ date="2013-11-03T17:35:00Z"
+ content="""
+Very strange: this is on a machine that I wiped and reinstalled just a few hours ago, it's a completely fresh Ubuntu 13.10 install with barely anything installed but the defaults. Git version is 1.8.3.2-1
+
+I initially just pulled git-annex from the Ubuntu repo. After that I grabbed a more recent version from https://launchpad.net/ubuntu/+source/git-annex/4.20131101/+build/5189754 which is showing the same behavior.
+
+\"git show git-annex\" indeed shows the commit creating the uuid.log file on the git-annex branch. master has just one commit, with description \"created repository\" and creates a \"uuid.log\" file. The contents of the master uuid.log are identical to the one in the git-annex branch.
+
+I'm currently in the middle of trying out a git-annex setup so I can't switch versions again right now, but given the above I imagine a fresh 13.10 VM should show the same behavior.
+"""]]
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_4_8e0f489305ce30ad578b9f8526e86416._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_4_8e0f489305ce30ad578b9f8526e86416._comment
new file mode 100644
index 000000000..c020fc3a8
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_4_8e0f489305ce30ad578b9f8526e86416._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 4"
+ date="2013-11-06T15:09:19Z"
+ content="""
+Intriguing -- I was able to reproduce this bug after installing the Ubuntu server ISO in a VM.
+
+Which is really strange, the only difference between this and my debootstrapped chroot should be the kernel..
+"""]]
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_5_c699034c8e02b2354516414d0ab73aab._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_5_c699034c8e02b2354516414d0ab73aab._comment
new file mode 100644
index 000000000..a323d7835
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_5_c699034c8e02b2354516414d0ab73aab._comment
@@ -0,0 +1,53 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 5"
+ date="2013-11-06T16:27:49Z"
+ content="""
+Running the prebuilt tarball build of git-annex, the bug does not occur.
+
+However, if I remove the git shipped with the prebuilt tarball, so it uses the system git, I do see the bug. So, it's apparently git version dependent.
+
+Also, I was able to reproduce it in a amd64 chroot. My other chroot was i386. Somehow architecture specific bug?
+
+---
+
+Instrumenting all calls to git to be logged with the full environment and command, I found this:
+
+<pre>
+GIT_INDEX_FILE='/home/foo/annex/.git/annex/index'
+--git-dir=/home/foo/annex/.git --work-tree=/home/foo/annex commit --quiet --allow-empty -m created repository
+</pre>
+
+This certainly looks like the index file setting for the git-annex branch is somehow leaking out past the branch commit operations. It continued setting that while setting up `gc.auto`; the next call to git after that stopped setting the index file.
+
+The only way I can see offhand this could possibly happen is due to an exception. It may be that on ubuntu an exception is thrown by code that runs a git command with the index file set, for whatever reason, and this causes the code that normally resets it back to not run.
+
+----
+
+Ok, found it! 
+
+<pre>
+\"withIndex entered\"
+
+*** Please tell me who you are.
+
+Run
+
+  git config --global user.email \"you@example.com\"
+  git config --global user.name \"Your Name\"
+
+to set your account's default identity.
+Omit --global to set the identity only in this repository.
+
+fatal: unable to auto-detect email address (got 'foo@darkstar.(none)')
+\"withIndex entered\"
+\"withIndex cleaned up\"
+</pre>
+
+Note lack of clean up after the first withIndex call. Thus leaving the environment passed to git polluted for further calls.
+
+This also explains why it's only happening on some systems, or with some versions of git. git's got all kinds of complexity around its username and email handling code.
+
+I have fixed this in git.
+"""]]
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_6_786cb7e643811dfd2496ceeff8f34f44._comment b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_6_786cb7e643811dfd2496ceeff8f34f44._comment
new file mode 100644
index 000000000..ea3e97e8e
--- /dev/null
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/comment_6_786cb7e643811dfd2496ceeff8f34f44._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 6"
+ date="2013-11-06T16:40:57Z"
+ content="""
+Ubuntu bug report about this: <https://bugs.launchpad.net/ubuntu/+source/git-annex/+bug/1248623>
+
+It should be pretty easy to backport the fix to the version in Ubuntu. The relevant git commits are ee23be55fd3e7e202bc721c124f78b79d1aba6df and 81117e8a9d19d4739d3773d0515006e1ea41c266
+"""]]
diff --git a/doc/bugs/Git_annex_add_fails_on_read-only_files.mdwn b/doc/bugs/Git_annex_add_fails_on_read-only_files.mdwn
new file mode 100644
index 000000000..26ee29e6d
--- /dev/null
+++ b/doc/bugs/Git_annex_add_fails_on_read-only_files.mdwn
@@ -0,0 +1,37 @@
+### Please describe the problem.
+
+Git annex cannot add/import files in folders without w or x permission
+
+Note that (as stated in the comments) this might not be a bug. The problem might somewhere within Git, because Git does not manage file permissions very well. I was just hoping that I could import large directory trees into git-annex with a simple call to "git annex import"; now it seems I have to fix their permissions first.
+
+### What steps will reproduce the problem?
+
+    $ cd /tmp
+    $ mkdir -p folder/subfolder
+    $ echo "some text" > folder/subfolder/some_file.txt
+    $ chmod 500 folder/subfolder
+    $ mkdir annex
+    $ cd annex
+    $ git init
+    $ git annex init "Testing git annex"
+    $ git annex import ../folder
+    Fails
+    $ chmod 600 ../folder/subfolder
+    $ git annex import ../folder
+    Fails
+    $ chmod 700 ../folder/subfolder
+    $ git annex import ../folder
+    Works. Subfolder now has 755 permissions
+
+### What version of git-annex are you using? On what operating system?
+
+    git-annex version: 4.20131106
+    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP Feeds Quvi TDFA CryptoHash
+    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+    remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+    local repository version: 3
+    default repository version: 3
+    supported repository versions: 3 4
+    upgrade supported from repository versions: 0 1 2
+
+    git version 1.8.4.3
diff --git a/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_1_d31018e8bf31d729ee9fee43a0a07934._comment b/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_1_d31018e8bf31d729ee9fee43a0a07934._comment
new file mode 100644
index 000000000..0a4e61bc5
--- /dev/null
+++ b/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_1_d31018e8bf31d729ee9fee43a0a07934._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T19:47:28Z"
+ content="""
+I cannot reproduce this problem on Linux, with version 4.20131106. I tried in both direct and indirect mode, on Linux. 
+
+I was, however, able to exactly reproduce the error message if I made the *directory* be not writable, and used indirect mode. This is because git-annex has to move the file the .git/annex/objects, and put a symlink in place, and so has to be allowed to write to the directory. Interestingly, direct mode does not have this limiation, although I doubt git-annex would ever be very useful when run in a directory you lack write permission to.
+"""]]
diff --git a/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_2_e38e7048749f890169cd0be602be6ee7._comment b/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_2_e38e7048749f890169cd0be602be6ee7._comment
new file mode 100644
index 000000000..610eea713
--- /dev/null
+++ b/doc/bugs/Git_annex_add_fails_on_read-only_files/comment_2_e38e7048749f890169cd0be602be6ee7._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlq4ClC5EMN1Vq1DpWXAqP5TiDnCK1mSfk"
+ nickname="Jonas"
+ subject="comment 2"
+ date="2013-11-27T18:05:02Z"
+ content="""
+Thank you for looking into this, and sorry about the low quality of the initial bug report. I now replaced the example by a better one.
+
+As you say, this might not be a bug. I was just not aware that migrating files into git-annex would mean forsaking their permissions.
+"""]]
diff --git a/doc/bugs/Glacier_remote_uploads_duplicates/comment_7_e96187bad3dae2f5f95118f6df87a1ec._comment b/doc/bugs/Glacier_remote_uploads_duplicates/comment_7_e96187bad3dae2f5f95118f6df87a1ec._comment
index 618f35765..26cbb5a47 100644
--- a/doc/bugs/Glacier_remote_uploads_duplicates/comment_7_e96187bad3dae2f5f95118f6df87a1ec._comment
+++ b/doc/bugs/Glacier_remote_uploads_duplicates/comment_7_e96187bad3dae2f5f95118f6df87a1ec._comment
@@ -6,5 +6,5 @@
  content="""
 Ok, I've merged the glacier branch into master. I would still be happy to see some testing of this before my next release (in a week).
 
-I guess I'll close this bug report. There are certianly still problems that can happen if there are multiple repositories all writing to glacier independently. Seems to me that one good way to deal with this is to set up a single remote that is configured to be a gateway to glacier.
+I guess I'll close this bug report. There are certainly still problems that can happen if there are multiple repositories all writing to glacier independently. Seems to me that one good way to deal with this is to set up a single remote that is configured to be a gateway to glacier.
 """]]
diff --git a/doc/bugs/Glacier_remote_uploads_duplicates/comment_8_34216b514a6fca788cfacb8579ce5311._comment b/doc/bugs/Glacier_remote_uploads_duplicates/comment_8_34216b514a6fca788cfacb8579ce5311._comment
new file mode 100644
index 000000000..67fd5354b
--- /dev/null
+++ b/doc/bugs/Glacier_remote_uploads_duplicates/comment_8_34216b514a6fca788cfacb8579ce5311._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="For those on Mac OS X"
+ date="2013-11-18T00:00:32Z"
+ content="""
+The duplicates script fails because the BSD/MacOS version of uniq doesn't support the -D option.
+
+You can work around this by installing the GNU version using Homebrew ('brew install coreutils') and then replacing the 'uniq' in the script with 'guniq' (Homebrew prefixes the coreutils with \"g\" by default).
+
+I seem to still be running in to this bug using git annex version 4.20131106 and 'git annex copy --to glacier' without the '--not --in glacier' flags.  It's not a problem to use the extra flags but I wasn't originally aware of this issue and the duplicates don't seem to always occur.  I'll do some more testing and see whether I can reliably predict what will create duplicates and what won't.
+"""]]
diff --git a/doc/bugs/Handling_of_files_inside_and_outside_archive_directory_at_the_same_time/comment_2_ead9fa75a12ef36be9a92637b144e74f._comment b/doc/bugs/Handling_of_files_inside_and_outside_archive_directory_at_the_same_time/comment_2_ead9fa75a12ef36be9a92637b144e74f._comment
index 5b355e070..2be39d451 100644
--- a/doc/bugs/Handling_of_files_inside_and_outside_archive_directory_at_the_same_time/comment_2_ead9fa75a12ef36be9a92637b144e74f._comment
+++ b/doc/bugs/Handling_of_files_inside_and_outside_archive_directory_at_the_same_time/comment_2_ead9fa75a12ef36be9a92637b144e74f._comment
@@ -6,7 +6,7 @@
  content="""
 This turns out to be much worse in direct mode than in indirect mode.
 
-In indirect mode, it only does extra work during the full startup scan. Suppose there are 3 files with the same content, 1, archive/2, and 3. It will download 1, and then will drop archive/2, and then will download 3. This certianly is not ideal, especially when the file content is large.
+In indirect mode, it only does extra work during the full startup scan. Suppose there are 3 files with the same content, 1, archive/2, and 3. It will download 1, and then will drop archive/2, and then will download 3. This certainly is not ideal, especially when the file content is large.
 
 In indirect mode, it continally and repeatedly downloads the drops the files, as long as it's running. Which is beyond unacceptable.
 
diff --git a/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp.mdwn b/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp.mdwn
new file mode 100644
index 000000000..4a8006f06
--- /dev/null
+++ b/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp.mdwn
@@ -0,0 +1,21 @@
+### Please describe the problem.
+As described earlier in [[tips/fully_encrypted_git_repositories_with_gcrypt]]
+
+### What steps will reproduce the problem?
+- A: use the webapp to create a new repository
+- A: add a remote server to the repository using the 'gcrypt' method
+- A: add a jabber account
+
+- B: use the webapp to create a new repository
+- B: add the jabber account
+- B: see the previously created 'cloud repository' with status 'not enabled'
+- B: click enable, see that the stored credentials are correct, and press "verify this server"
+- B: enter the ssh password twice
+- B: get redirected to a blank screen (on the url /config/repository/enable/gcrypt/UUID "x"?auth=y)
+
+The assistent logfiles show nothing after the "Your public key has been saved in", the server shows that no public key for B was added to the account.
+
+This is with git-annex installed on the remote server; without it the process gets stuck after clicking "encrypt repository" in step 2, it will just indefinitely keep prompting for the SSH password.
+
+### What version of git-annex are you using? On what operating system?
+Latest nightly build on ubuntu 13.10
diff --git a/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp/comment_1_17814787e333d15da3ab4e57c7d31d4b._comment b/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp/comment_1_17814787e333d15da3ab4e57c7d31d4b._comment
new file mode 100644
index 000000000..5bd45d686
--- /dev/null
+++ b/doc/bugs/Impossible_to_enable_an_existing_gcrypt_repo_in_the_webapp/comment_1_17814787e333d15da3ab4e57c7d31d4b._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-13T16:51:40Z"
+ content="""
+I've tried to reproduce this, and cannot; it enabled the repository without trouble.
+
+Also, I have never seen the webapp fail with a blank screen, so that's strange.
+
+I think you need to show your `~/annex/.git/annex/daemon.log` from B.
+"""]]
diff --git a/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__.mdwn b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__.mdwn
new file mode 100644
index 000000000..9b5d52220
--- /dev/null
+++ b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__.mdwn
@@ -0,0 +1,44 @@
+### Please describe the problem.
+Incorrect merge of direct repos.
+
+### What steps will reproduce the problem?
+
+[[!format sh """
+# setting up stuff
+test/a$ git init
+test/a$ git annex init
+test/a$ git annex direct
+test/a$ touch firstfile
+test/a$ git annex add firstfile
+$ git clone test/a
+$ mv a test/b
+test/b$ git annex direct
+
+# actual scenario
+test/b$ echo bbbb > f
+test/b$ git annex add f
+test/b$ git annex sync
+test/a$ mkdir f
+test/a$ echo aaaa > f/f
+test/a$ git annex add f/f
+test/a$ git annex sync
+test/b$ git annex sync
+test/b$ rm f
+test/b$ git annex sync
+test/b$ ls
+test/b$ firstfile
+test/b$ f.variant-SHA256E-s5--4551db5fd4d56e27be71a8a943070cfaa4342b8e960a326e2d6427b3aa0a5a48.variant-43f5
+test/a$ git annex sync  # A's f/f is no longer to be found
+"""]]
+
+### What version of git-annex are you using? On what operating system?
+[[!format sh """
+git-annex version: 4.20131031-g7d99d14
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi TDFA CryptoHash
+key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+
+Linux ceilingcat 3.11.6-1-ARCH #1 SMP PREEMPT Fri Oct 18 23:22:36 CEST 2013 x86_64 GNU/Linux
+"""]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_1_15c354c4841d364e78882d2b46a0a764._comment b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_1_15c354c4841d364e78882d2b46a0a764._comment
new file mode 100644
index 000000000..53c9f7915
--- /dev/null
+++ b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_1_15c354c4841d364e78882d2b46a0a764._comment
@@ -0,0 +1,66 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-14T17:06:50Z"
+ content="""
+I verify this bug. And it's specific to direct mode as you say. Here is a shell script which automates the proccess:
+
+[[!format sh \"\"\"
+#!/bin/sh
+set -e
+mkdir test
+cd test
+git init a
+
+cd a
+git annex init
+git annex direct
+touch firstfile
+git annex add firstfile
+git annex sync # think this was left out of recipe
+
+cd ..
+
+git clone a b
+cd b
+git annex direct
+echo bbbb > f
+git annex add f
+git annex sync || true
+cd ..
+cd a
+mkdir f
+echo aaaa > f/f
+git annex add f/f
+git annex sync || true
+cd ..
+cd b
+git annex sync
+echo \"after merge:\"
+ls
+\"\"\"]]
+
+At this point, b only has the file version of f; the directory form has been removed. (Syncing to a of course then does the same thing there.)
+
+And from the trascript, we can see what's going on:
+
+<pre>
+Adding f/f
+CONFLICT (directory/file): There is a directory with name f in HEAD. Adding f as f~refs_heads_synced_master
+Automatic merge failed; fix conflicts and then commit the result.
+(Recording state in git...)
+f: needs merge
+[master 0600854] git-annex automatic merge conflict fix
+
+  Merge conflict was automatically resolved; you may want to examine the result.
+</pre>
+
+The problem seems to be that direct mode merge does not find the `f~refs_heads_synced_master` created by the merge, so fails to copy it from the temp merge tree into the work tree.
+
+`Command.Sync.cleanConflictCruft` is relevant, but was only made to work in indirect mode, it seems.
+
+----
+
+Obviously, if someone runs into this bug and seems to lose data, they can get the data back by reverting the changes from the automatic merge. Direct mode does preserve file contents when removing them from the work tree in a merge.
+"""]]
diff --git a/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_2_8bc496226a977dbeeb1ce3f06122f1c2._comment b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_2_8bc496226a977dbeeb1ce3f06122f1c2._comment
new file mode 100644
index 000000000..f9d3c7ffe
--- /dev/null
+++ b/doc/bugs/Incorrect_merge__44___direct_repos___40__2__41__/comment_2_8bc496226a977dbeeb1ce3f06122f1c2._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 2"
+ date="2013-11-15T17:39:37Z"
+ content="""
+My initial guess was wrong.. This is not actually a bug in conflicted merge resolution at all.
+
+The bug is that in direct mode, it diffs the old and new tree when doing a normal merge, so see what files in the work tree need to be changed. This was written to go through the diff and replay the deletes and adds. In this case, since f/f and f are different items, they can appear in either order in the diff But the code only worked when f was first deleted, and f/f was then added. And it turns out that in this case, the diff had the two items the other way around.
+
+So, I think it needs to do 2 passes, first deleting and then adding.
+"""]]
diff --git a/doc/bugs/Incorrect_merge___40__a_special_case__41__.mdwn b/doc/bugs/Incorrect_merge___40__a_special_case__41__.mdwn
new file mode 100644
index 000000000..8e25ed6cb
--- /dev/null
+++ b/doc/bugs/Incorrect_merge___40__a_special_case__41__.mdwn
@@ -0,0 +1,48 @@
+### Please describe the problem.
+(Minor issue.)
+
+Incorrect merge of direct repos in the special case where at repo A a symlink to a file whose contents aren't yet available, are overwritten, while at repo B the file is deleted.
+
+Result: file is deleted on both side.
+
+Expected: B.f is gone, A.f is still present
+
+### What steps will reproduce the problem?
+
+[[!format sh """
+# setting up stuff
+test/a$ git init
+test/a$ git annex init
+test/a$ git annex direct
+test/a$ touch firstfile
+test/a$ git annex add firstfile
+$ git clone test/a
+$ mv a test/b
+test/b$ git annex direct
+
+# actual scenario
+test/b$ echo bbbb > f
+test/b$ git annex add f
+test/b$ git annex sync
+test/a$ git annex sync
+test/a$ echo aaaa > f
+test/a$ git annex add f
+test/a$ git annex sync
+test/b$ rm f
+test/b$ git annex sync
+test/a$ git annex sync
+# test/a/f is now gone, lost
+"""]]
+
+### What version of git-annex are you using? On what operating system?
+[[!format sh """
+git-annex version: 4.20131031-g7d99d14
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi TDFA CryptoHash
+key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+
+Linux ceilingcat 3.11.6-1-ARCH #1 SMP PREEMPT Fri Oct 18 23:22:36 CEST 2013 x86_64 GNU/Linux
+"""]]
+
+> [[fixed|done]]; direct mode now freezes the content directory as indirect
+> mode already did. fsck will fix up the permissions too. --[[Joey]]
diff --git a/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_1_c80418d76b501c688e3a9fb4831520fd._comment b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_1_c80418d76b501c688e3a9fb4831520fd._comment
new file mode 100644
index 000000000..0594ddabe
--- /dev/null
+++ b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_1_c80418d76b501c688e3a9fb4831520fd._comment
@@ -0,0 +1,41 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-14T17:10:55Z"
+ content="""
+I suspect this might be the same underlying problem as [[bugs/Incorrect merge, direct repos (2)]]. However, I cannot reproduce it using the recipe given.. perhaps something was left out?
+
+I wrote this shell script to try to codify the recipe in a runnable form:
+
+[[!format sh \"\"\"
+#!/bin/sh
+set -e
+mkdir test
+cd test
+git init a
+
+cd a
+git annex init
+git annex direct
+touch firstfile
+git annex add firstfile
+git annex sync # think this was left out of recipe
+
+cd ..
+
+git clone a b
+cd b
+git annex direct
+echo bbbb > f
+git annex add f
+git annex sync || true
+cd ..
+cd a
+echo aaaa > f
+git annex add f
+git annex sync
+\"\"\"]]
+
+At this point, a has 2 variants of f, and no amount of syncing in either repo will cause either variant to go away.
+"""]]
diff --git a/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_2_8b2a188696f46819f6e3f0e9660362d2._comment b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_2_8b2a188696f46819f6e3f0e9660362d2._comment
new file mode 100644
index 000000000..39bb90877
--- /dev/null
+++ b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_2_8b2a188696f46819f6e3f0e9660362d2._comment
@@ -0,0 +1,45 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlWskoNgUB7r70OXglR-4iKI4bOuPJb-xg"
+ nickname="Tim"
+ subject="comment 2"
+ date="2013-11-14T18:06:55Z"
+ content="""
+You were missing a: test/a$ git annex sync
+
+This did the trick on my system
+[[!format sh \"\"\"
+#!/bin/sh
+set -e
+mkdir test
+cd test
+git init a
+
+cd a
+git annex init
+git annex direct
+touch firstfile
+git annex add firstfile
+git annex sync # think this was left out of recipe  # indeed it was
+
+cd ..
+
+git clone a b
+cd b
+git annex direct
+echo bbbb > f
+git annex add f
+git annex sync || true  # why add a || true?
+cd ../a
+git annex sync
+echo aaaa > f
+git annex add f
+git annex sync
+cd ../b
+rm f
+git annex sync
+ls
+cd ../a
+git annex sync
+ls
+\"\"\"]]
+"""]]
diff --git a/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_3_8cdbb1fda506b9e53a0e9ab88b2569c1._comment b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_3_8cdbb1fda506b9e53a0e9ab88b2569c1._comment
new file mode 100644
index 000000000..ce5c144e1
--- /dev/null
+++ b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_3_8cdbb1fda506b9e53a0e9ab88b2569c1._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 3"
+ date="2013-11-15T17:48:42Z"
+ content="""
+Hmm. In your script, when you run `git annex sync` in a and then `echo aaaa > f`, f already exists at that point as a symlink. This actually ends up following the link and writing to .git/annex/objects. (fsck will detect that junk has been written there)
+
+That's a bug on its own; seems like direct mode is neglecting to lock down the .git/annex/objects directories to prevent writing to them like this.
+
+----
+
+However, this means that your script does not demonstrate the bug you originally reported. 
+You remove b/f and sync, and since a/f has not been changed, the deleting is correctly synced to a, removing a/f.
+"""]]
diff --git a/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_4_9d74e2854a5d77f0f793f56fa0cff9e2._comment b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_4_9d74e2854a5d77f0f793f56fa0cff9e2._comment
new file mode 100644
index 000000000..c7bb02765
--- /dev/null
+++ b/doc/bugs/Incorrect_merge___40__a_special_case__41__/comment_4_9d74e2854a5d77f0f793f56fa0cff9e2._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 4"
+ date="2013-11-15T17:52:38Z"
+ content="""
+Looking back at the original bug description:
+
+\"repo A a symlink to a file whose contents aren't yet available, are overwritten, while at repo B the file is deleted.\"
+
+I think the \"overwritten\" is key. I suspect you were always doing echo > f where f was a symlink, and this does not actually overwrite the symlink, it just puts data (that fsck will reject) into the annex.
+
+So, proceeding as if the real bug here is the ability to write through symlink in direct mode, unless told otherwise..
+"""]]
diff --git a/doc/bugs/Incorrect_version_of_Git_Annex___40__1.0.52__41___as_seen_by_Android.mdwn b/doc/bugs/Incorrect_version_of_Git_Annex___40__1.0.52__41___as_seen_by_Android.mdwn
new file mode 100644
index 000000000..95db65e25
--- /dev/null
+++ b/doc/bugs/Incorrect_version_of_Git_Annex___40__1.0.52__41___as_seen_by_Android.mdwn
@@ -0,0 +1,24 @@
+### Please describe the problem.
+
+Git Annex is listed as of version 1.0.52 if you check out its entry in the list of applications in the Android configuration.  I guess that one is of the terminal app which kickstarts the annex.
+
+### What steps will reproduce the problem?
+
+install apk
+
+### What version of git-annex are you using? On what operating system?
+
+android
+5.2013whatever
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/JSON_output_broken_with___34__git_annex_sync__34__/comment_1_380a49b3c132f9f529729a1cb5a69621._comment b/doc/bugs/JSON_output_broken_with___34__git_annex_sync__34__/comment_1_380a49b3c132f9f529729a1cb5a69621._comment
index f0eff45c1..d1ad05842 100644
--- a/doc/bugs/JSON_output_broken_with___34__git_annex_sync__34__/comment_1_380a49b3c132f9f529729a1cb5a69621._comment
+++ b/doc/bugs/JSON_output_broken_with___34__git_annex_sync__34__/comment_1_380a49b3c132f9f529729a1cb5a69621._comment
@@ -4,5 +4,5 @@
  subject="comment 1"
  date="2012-11-27T21:13:08Z"
  content="""
-Yeah, so git-annex has --json as a option available to any command, but the set of commands where it's actually useful is rather smaller, and certianly does not include this one. In general there are quite a lot of places where third-party program output is allowed to show through to provide necessary progress or debugging output, and that of course makes the json mode invalid.
+Yeah, so git-annex has --json as a option available to any command, but the set of commands where it's actually useful is rather smaller, and certainly does not include this one. In general there are quite a lot of places where third-party program output is allowed to show through to provide necessary progress or debugging output, and that of course makes the json mode invalid.
 """]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop.mdwn b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop.mdwn
new file mode 100644
index 000000000..63f423e2c
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop.mdwn
@@ -0,0 +1,39 @@
+### Please describe the problem.
+Pairing over my local network doesn't work.  The pairing process never finishes.  The log shows that the same PairMsg messages are repeated endlessly.
+
+### What steps will reproduce the problem?
+
+
+### What version of git-annex are you using? On what operating system?
+I'm on Ubuntu Raring 13.04.  I installed git-annex 4.20131024 from the Precise PPA.  It is working fine with a remote ssh repo, just not local pairing.
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+[2013-11-01 16:55:21 CDT] main: Pairing in progress
+[2013-11-01 16:55:55 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"Onyx\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDBT0Y6TTzTg8nWwonmgUPPwJmPIaJzfEoJl8DbuylpgXqGCQ4doJXuvBODHIehPfyMr1xCWqNlNNLkcWg/a/eHFceyt3IlcD9XaZ1aKPzPmpjYKKf5amiYd6mAssw8zFaZUvwaXkNuHZpXVZyg6C6TkT6kdfln+6fOJZpSGQzksy0jka/Rzx0KXjsp3oqO4tQJbC7AX0nvmD0zvLtyCURzfGV+n2IqQxpPf2nP75Evt8jamcuqm6pWoe+hj9zjGytIXpSKe35wzRwUAUrjgmZ9NweuWfi2uMPJlDv8/n+Q3HyjygA+GzixBGuYXDt1CD8ISZvuoygS+9+jeY9uYH8b me@Onyx\\n\", pairUUID = UUID \"834b4f39-ca66-4baf-9323-57ef7058d7d0\"},IPv4Addr 2281744576), verifiableDigest = \"8d5d380542f7377f09a4584a38b0dbcea9ea215c\"})"
+[2013-11-01 16:55:56 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"kubbie\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCvBEWT+AiAmehOFyTQWlSdwDs7DDbkw7rfZ4W/IeG5awZjMgT5BefIv9cmar8vGIIEFMZLpf8cL3xIargDz0xE2wuqj5CLkdz+DKp5f2FGs11Ax/62DZr+eCiVtPnwijFw0Cz0wMRzkN93uedrvzP/KkNRcczgWh3aZqn8WxlkCia1fyykm/pP3W80MNkiJYX5vXpu1NCV5KLu+UXQzKhM2njOauJ3W5wsMvSl8faZIpEmKVCD3BMDDruxTIxggA3kt9GCGvIbPawy+fGOpp/j6pHqnX3GB2kkT47RIZKYEv99HuLyvea+oY5R11FsC2yYY3ujIdUU0fXnV8pvrqSv me@kubbie\\n\", pairUUID = UUID \"fd6a6858-76c9-4eea-b733-9359c7313e72\"},IPv4Addr 1879091392), verifiableDigest = \"cbd8197c3d78c8c68bb30f63aa974cd88dd0fb13\"})"
+[2013-11-01 16:55:57 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"Onyx\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDBT0Y6TTzTg8nWwonmgUPPwJmPIaJzfEoJl8DbuylpgXqGCQ4doJXuvBODHIehPfyMr1xCWqNlNNLkcWg/a/eHFceyt3IlcD9XaZ1aKPzPmpjYKKf5amiYd6mAssw8zFaZUvwaXkNuHZpXVZyg6C6TkT6kdfln+6fOJZpSGQzksy0jka/Rzx0KXjsp3oqO4tQJbC7AX0nvmD0zvLtyCURzfGV+n2IqQxpPf2nP75Evt8jamcuqm6pWoe+hj9zjGytIXpSKe35wzRwUAUrjgmZ9NweuWfi2uMPJlDv8/n+Q3HyjygA+GzixBGuYXDt1CD8ISZvuoygS+9+jeY9uYH8b me@Onyx\\n\", pairUUID = UUID \"834b4f39-ca66-4baf-9323-57ef7058d7d0\"},IPv4Addr 2281744576), verifiableDigest = \"8d5d380542f7377f09a4584a38b0dbcea9ea215c\"})"
+[2013-11-01 16:55:58 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"kubbie\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCvBEWT+AiAmehOFyTQWlSdwDs7DDbkw7rfZ4W/IeG5awZjMgT5BefIv9cmar8vGIIEFMZLpf8cL3xIargDz0xE2wuqj5CLkdz+DKp5f2FGs11Ax/62DZr+eCiVtPnwijFw0Cz0wMRzkN93uedrvzP/KkNRcczgWh3aZqn8WxlkCia1fyykm/pP3W80MNkiJYX5vXpu1NCV5KLu+UXQzKhM2njOauJ3W5wsMvSl8faZIpEmKVCD3BMDDruxTIxggA3kt9GCGvIbPawy+fGOpp/j6pHqnX3GB2kkT47RIZKYEv99HuLyvea+oY5R11FsC2yYY3ujIdUU0fXnV8pvrqSv me@kubbie\\n\", pairUUID = UUID \"fd6a6858-76c9-4eea-b733-9359c7313e72\"},IPv4Addr 1879091392), verifiableDigest = \"cbd8197c3d78c8c68bb30f63aa974cd88dd0fb13\"})"
+[2013-11-01 16:55:59 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"Onyx\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDBT0Y6TTzTg8nWwonmgUPPwJmPIaJzfEoJl8DbuylpgXqGCQ4doJXuvBODHIehPfyMr1xCWqNlNNLkcWg/a/eHFceyt3IlcD9XaZ1aKPzPmpjYKKf5amiYd6mAssw8zFaZUvwaXkNuHZpXVZyg6C6TkT6kdfln+6fOJZpSGQzksy0jka/Rzx0KXjsp3oqO4tQJbC7AX0nvmD0zvLtyCURzfGV+n2IqQxpPf2nP75Evt8jamcuqm6pWoe+hj9zjGytIXpSKe35wzRwUAUrjgmZ9NweuWfi2uMPJlDv8/n+Q3HyjygA+GzixBGuYXDt1CD8ISZvuoygS+9+jeY9uYH8b me@Onyx\\n\", pairUUID = UUID \"834b4f39-ca66-4baf-9323-57ef7058d7d0\"},IPv4Addr 2281744576), verifiableDigest = \"8d5d380542f7377f09a4584a38b0dbcea9ea215c\"})"
+[2013-11-01 16:56:00 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"kubbie\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCvBEWT+AiAmehOFyTQWlSdwDs7DDbkw7rfZ4W/IeG5awZjMgT5BefIv9cmar8vGIIEFMZLpf8cL3xIargDz0xE2wuqj5CLkdz+DKp5f2FGs11Ax/62DZr+eCiVtPnwijFw0Cz0wMRzkN93uedrvzP/KkNRcczgWh3aZqn8WxlkCia1fyykm/pP3W80MNkiJYX5vXpu1NCV5KLu+UXQzKhM2njOauJ3W5wsMvSl8faZIpEmKVCD3BMDDruxTIxggA3kt9GCGvIbPawy+fGOpp/j6pHqnX3GB2kkT47RIZKYEv99HuLyvea+oY5R11FsC2yYY3ujIdUU0fXnV8pvrqSv me@kubbie\\n\", pairUUID = UUID \"fd6a6858-76c9-4eea-b733-9359c7313e72\"},IPv4Addr 1879091392), verifiableDigest = \"cbd8197c3d78c8c68bb30f63aa974cd88dd0fb13\"})"
+[2013-11-01 16:56:01 CDT] PairListener: received "PairMsg (Verifiable {verifiableVal = (PairReq,PairData {remoteHostName = Just \"Onyx\", remoteUserName = \"me\", remoteDirectory = \"~/annex\", remoteSshPubKey = \"ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDBT0Y6TTzTg8nWwonmgUPPwJmPIaJzfEoJl8DbuylpgXqGCQ4doJXuvBODHIehPfyMr1xCWqNlNNLkcWg/a/eHFceyt3IlcD9XaZ1aKPzPmpjYKKf5amiYd6mAssw8zFaZUvwaXkNuHZpXVZyg6C6TkT6kdfln+6fOJZpSGQzksy0jka/Rzx0KXjsp3oqO4tQJbC7AX0nvmD0zvLtyCURzfGV+n2IqQxpPf2nP75Evt8jamcuqm6pWoe+hj9zjGytIXpSKe35wzRwUAUrjgmZ9NweuWfi2uMPJlDv8/n+Q3HyjygA+GzixBGuYXDt1CD8ISZvuoygS+9+jeY9uYH8b me@Onyx\\n\", pairUUID = UUID \"834b4f39-ca66-4baf-9323-57ef7058d7d0\"},IPv4Addr 2281744576), verifiableDigest = \"8d5d380542f7377f09a4584a38b0dbcea9ea215c\"})"
+...and so on and so on...
+# End of transcript or log.
+"""]]
+
+> I was able to reproduce something very like this by starting
+> pairing separately on both computers under poor network conditions (ie,
+> weak wifi on my front porch).
+> 
+> So, I've made a new PairReq message that has not been seen before 
+> always make the alert pop up, even if the assistant thinks it is
+> in the middle of its own pairing process (or even another pairing process
+> with a different box on the LAN).
+>
+> (This shouldn't cause a rogue PairAck to disrupt a pairing process part
+> way through.)
+> 
+> [[done]] --[[Joey]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_1_b8c485bafd98be8c21595597af361255._comment b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_1_b8c485bafd98be8c21595597af361255._comment
new file mode 100644
index 000000000..39587ee90
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_1_b8c485bafd98be8c21595597af361255._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 1"
+ date="2013-11-01T23:10:12Z"
+ content="""
+Also, when I initiate the pairing process on one computer only, I can see the PairMsg being constantly received in the other computer's log, but the prompt to finish pairing never appears.
+"""]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_2_bc63489334f44a423645021415ffe196._comment b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_2_bc63489334f44a423645021415ffe196._comment
new file mode 100644
index 000000000..f10b16f3c
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_2_bc63489334f44a423645021415ffe196._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 2"
+ date="2013-11-01T23:27:24Z"
+ content="""
+Well I installed the 1 Nov release from the tarball and then it picked up the pair request from the other system.  I don't know if it was a bug in the previous version or something to do with the PPA.  It's weird that the assistant just wasn't doing anything about the pair request it received.
+
+Thanks for your work on git-annex assistant.
+"""]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_3_6345b174d04b6613c2c55a6ec9e50c21._comment b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_3_6345b174d04b6613c2c55a6ec9e50c21._comment
new file mode 100644
index 000000000..a7eff6744
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_3_6345b174d04b6613c2c55a6ec9e50c21._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T19:02:55Z"
+ content="""
+There is something a little strange in the logs. It shows both Onyx and kubbie are sending PairReqs. Probably one of those is the local computer, logging its own broadcast messages which loop back to it. But normally in pairing, one side starts the pairing process with a PairReq, and the other side pops up an alert and continues the process with a PairAck. It's not normal for both sides to request that pairing start.
+
+Is it possible that you started pairing on both computers separately?
+
+I tried doing that with gnu and darkstar. First I started pairing on gnu. darkstar saw the pair request, but I ignored the alert message about that, and went  and started a separate pairing process on darkstar. gnu never showed an alert message for that; it ignored darkstar's PairReqs since it was sending its own.
+
+It's unlikely you'd ignore the alert, but the same thing could happen if the two computers were not able to communicate over the network initially, and pairing were started on both separately. So neither gets a chance to see the other's PairReq and show the alert. Even when they came into communication, they'd each ignore the other's PairReq.
+
+So, that seems like a bug..
+"""]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_4_f39ec6c3d5a016b3c5260162c0b42177._comment b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_4_f39ec6c3d5a016b3c5260162c0b42177._comment
new file mode 100644
index 000000000..cacbad03f
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_4_f39ec6c3d5a016b3c5260162c0b42177._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 4"
+ date="2013-11-02T22:52:31Z"
+ content="""
+I did indeed try to pair from both systems.  What happened was, after I started the pair request, I went to the other system, and there was no pair request listed.  So I misunderstood the directions and thought I was supposed to go ahead and enter the same password into the other system.  (It says that pairing will complete as soon as the password is entered on the other system, so it seems reasonable to try that.)  Then both systems were constantly issuing pair requests, but neither system was responding to the requests, even though it was receiving them.
+
+Both systems were always on the network and always able to communicate over it.  The bug went away when I upgraded to the 1 Nov release...but then I had some very confusing issues with partially-paired repos from different git-annex versions...I ended up having to start git-annex over from scratch on both systems with the 1 Nov build.
+
+So I'm not sure where to go from here with this bug.  Thanks for your help.
+"""]]
diff --git a/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_5_ca0c5ef6e6a6d2c4b64430ac68370b6a._comment b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_5_ca0c5ef6e6a6d2c4b64430ac68370b6a._comment
new file mode 100644
index 000000000..413ca952e
--- /dev/null
+++ b/doc/bugs/Local_pairing_fails:_received_PairMsg_loop/comment_5_ca0c5ef6e6a6d2c4b64430ac68370b6a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 5"
+ date="2013-11-02T22:55:42Z"
+ content="""
+Oh, now I see your comment up there that you fixed it.  Awesome.  :)
+"""]]
diff --git a/doc/bugs/Lost_S3_Remote/comment_1_6e80e6db6671581d471fc9a54181c04c._comment b/doc/bugs/Lost_S3_Remote/comment_1_6e80e6db6671581d471fc9a54181c04c._comment
index b4f7bdc3c..d6595ad5b 100644
--- a/doc/bugs/Lost_S3_Remote/comment_1_6e80e6db6671581d471fc9a54181c04c._comment
+++ b/doc/bugs/Lost_S3_Remote/comment_1_6e80e6db6671581d471fc9a54181c04c._comment
@@ -6,5 +6,5 @@
  content="""
 Despite `status` listing S3 support, your git-annex is actually built with S3stub, probably because it failed to find the necessary S3 module at build time. Rebuild git-annex and watch closely, you'll see \"** building without S3 support\". Look above that for the error and fix it.
 
-It was certianly a bug that it showed S3 as supported when built without it. I've fixed that.
+It was certainly a bug that it showed S3 as supported when built without it. I've fixed that.
 """]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__.mdwn b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__.mdwn
new file mode 100644
index 000000000..2875e63e4
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__.mdwn
@@ -0,0 +1,23 @@
+### Please describe the problem.
+
+Creating a USB repo fails with a GPG error.
+
+### What steps will reproduce the problem?
+
+  * Build git-annex and git-annex assistant using the instructions at https://gist.github.com/calmyournerves/7144127
+  * Run git-annex app to launch web interface
+  * Create local repo using web interface
+  * Try to create USB repo using web interface
+
+### What version of git-annex are you using? On what operating system?
+
+git-annex version 4.20131105-g136b030 on Mac OS 10.9 Mavericks.
+
+### Please provide any additional information below.
+
+[[!format sh """
+07/Nov/2013:06:51:07 +1100 [Error#yesod-core] user error (gpg ["--batch","--no-tty","--use-agent","--quiet","--trust-model","always","--with-colons","--list-secret-keys","--fixed-list-mode"] exited 5) @(yesod-core-1.2.4.5:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+"""]]
+
+> [[fixed|done]]; it seems that this was a local build issue ad does not
+> affect the autobuild. --[[Joey]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_1_0b4dcedc58e5071733e1239490aed2ea._comment b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_1_0b4dcedc58e5071733e1239490aed2ea._comment
new file mode 100644
index 000000000..34d8d94b1
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_1_0b4dcedc58e5071733e1239490aed2ea._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="Updated version 4.20131105-g136b030 seems to work"
+ date="2013-11-07T20:28:55Z"
+ content="""
+I've updated to the latest version as of 12 hours ago and I was able to create a USB repo on two computers.  4.20131105-g136b030 showing on the web app but 20131106 on the command line.
+
+Is there an easy way of checking the repo is correctly encrypted?  I didn't see anything about encrypting (now the previous error has disappeared) when creating the repo - is this what I should expect?
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_2_1cb1ef0292a3357874b461a77c13373e._comment b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_2_1cb1ef0292a3357874b461a77c13373e._comment
new file mode 100644
index 000000000..83e0b2317
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_2_1cb1ef0292a3357874b461a77c13373e._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 2"
+ date="2013-11-08T17:36:53Z"
+ content="""
+USB repos are not set up encryption unless you explicitly request it.
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_3_e5ec1e3ab304d738e3b0847287a47af4._comment b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_3_e5ec1e3ab304d738e3b0847287a47af4._comment
new file mode 100644
index 000000000..0b3a804b9
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_erro_when_creating_USB_repo___40__solved__41__/comment_3_e5ec1e3ab304d738e3b0847287a47af4._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="Yes, I just figured that out"
+ date="2013-11-08T22:09:40Z"
+ content="""
+I figured it out a couple of hours ago when I was able to use the existing USB repo on a new computer that doesn't have any of my private keys on it.
+
+I didn't see an option in the web interface to use encryption - is it command line only?
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__.mdwn b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__.mdwn
new file mode 100644
index 000000000..5c70527fd
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__.mdwn
@@ -0,0 +1,28 @@
+### Please describe the problem.
+
+Creating a remote S3 repository using the git-annex assistant web interface fails with a GPG error.  (I'm also getting a GPG error trying to create a USB repo but it's slightly different so I'll post a different bug.)
+
+### What steps will reproduce the problem?
+
+  * Build git-annex and git-annex assistant using the instructions at https://gist.github.com/calmyournerves/7144127
+  * Run git-annex app to launch web interface
+  * Create local repo using web interface
+  * Try to create encrypted S3 remote repo using web interface
+
+### What version of git-annex are you using? On what operating system?
+
+git-annex version 4.20131105-g136b030 on MacOS 10.9 Mavericks.
+
+### Please provide any additional information below.
+
+[[!format sh """
+
+(encryption setup) dyld: Library not loaded: @rpath/libz.1.2.8.dylib
+  Referenced from: /Applications/git-annex.app/Contents/MacOS/bundle/gpg
+  Reason: image not found
+07/Nov/2013:06:38:27 +1100 [Error#yesod-core] user error (gpg ["--batch","--no-tty","--use-agent","--quiet","--trust-model","always","--gen-random","--armor","1","512"] exited 5) @(yesod-core-1.2.4.5:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+
+"""]]
+
+> [[fixed|done]]; it seems that this was a local build issue ad does not
+> affect the autobuild. --[[Joey]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_1_d95accb43bd18cc9acbbf1d4069f86b3._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_1_d95accb43bd18cc9acbbf1d4069f86b3._comment
new file mode 100644
index 000000000..0f1e34e31
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_1_d95accb43bd18cc9acbbf1d4069f86b3._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="S3 works without encryption"
+ date="2013-11-06T21:09:26Z"
+ content="""
+Not surprisingly, S3 repos work without encryption.
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_2_452a3c524974832f0742efb00df4d576._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_2_452a3c524974832f0742efb00df4d576._comment
new file mode 100644
index 000000000..6b3ca2a0b
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_2_452a3c524974832f0742efb00df4d576._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="Still fails with git-annex version 4.20131105-g136b030"
+ date="2013-11-07T20:32:09Z"
+ content="""
+Updating seems to have fixed my other problem with creating a USB repo but still fails when trying to create an encrypted S3 repo.
+
+    (encryption setup) dyld: Library not loaded: @rpath/libz.1.2.8.dylib
+      Referenced from: /Applications/git-annex.app/Contents/MacOS/bundle/gpg
+      Reason: image not found
+    08/Nov/2013:07:30:11 +1100 [Error#yesod-core] user error (gpg [\"--batch\",\"--no-tty\",\"--use-agent\",\"--quiet\",\"--trust-model\",\"always\",\"--gen-random\",\"--armor\",\"1\",\"512\"] exited 5) @(yesod-core-1.2.4.5:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_3_f8f6d1e0065e5ba56cd405b1c021ca09._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_3_f8f6d1e0065e5ba56cd405b1c021ca09._comment
new file mode 100644
index 000000000..e2ae9c3dc
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_3_f8f6d1e0065e5ba56cd405b1c021ca09._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 3"
+ date="2013-11-08T17:38:40Z"
+ content="""
+Looks like it failed to include libz.1.2.8.dylib in the bundle for some reason despite gpg needing it.
+
+I don't really see the point in building an app bundle if you're going to install it back to the same machine you built it on. It's much easier to just `cabal install git-annex` in this case.
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_4_b524649cee751532d20a4894d71c5cf3._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_4_b524649cee751532d20a4894d71c5cf3._comment
new file mode 100644
index 000000000..8c7450ca6
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_4_b524649cee751532d20a4894d71c5cf3._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="Maybe I'm missing something..."
+ date="2013-11-08T22:12:04Z"
+ content="""
+But does cabal install git-annex install the assistant?  On the Mac, I use the app bundle to launch the web interface from my applications folder.
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_5_8312ba868ef616ec00563446c9c3464f._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_5_8312ba868ef616ec00563446c9c3464f._comment
new file mode 100644
index 000000000..f94f2d9c8
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_5_8312ba868ef616ec00563446c9c3464f._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="To answer my own question - &quot;git annex webapp&quot;"
+ date="2013-11-09T00:10:28Z"
+ content="""
+Will open the web app from the command line.
+
+But now I get a different error trying to create an encrypted S3 repo.
+
+    (encryption setup) 09/Nov/2013:11:08:56 +1100 [Error#yesod-core] user error (gpg [\"--quiet\",\"--trust-model\",\"always\",\"--gen-random\",\"--armor\",\"1\",\"512\"] exited 127) @(yesod-core-1.2.4.5:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_6_1af75c691d27c97397f1901f7c2483b0._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_6_1af75c691d27c97397f1901f7c2483b0._comment
new file mode 100644
index 000000000..19313d9a7
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_6_1af75c691d27c97397f1901f7c2483b0._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="Works with git annex on command line"
+ date="2013-11-09T20:18:38Z"
+ content="""
+git annex initremote cloud type=S3 keyid=key correct creates an encrypted S3 repo and I'm able to upload files.
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_7_e519df252875de87c4ef5b727f033bdf._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_7_e519df252875de87c4ef5b727f033bdf._comment
new file mode 100644
index 000000000..a67c59451
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_7_e519df252875de87c4ef5b727f033bdf._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 7"
+ date="2013-11-15T19:00:25Z"
+ content="""
+It would be useful if you could test with the 10.9 build now available in [[install/OSX]].
+"""]]
diff --git a/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_8_4bb959e2659991cd392853e8beacf708._comment b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_8_4bb959e2659991cd392853e8beacf708._comment
new file mode 100644
index 000000000..cff7e9dee
--- /dev/null
+++ b/doc/bugs/Mac_OS_10.9_GPG_error_adding_S3_repo___40__solved__41__/comment_8_4bb959e2659991cd392853e8beacf708._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="comment 8"
+ date="2013-11-15T21:31:40Z"
+ content="""
+Thanks Joey - I was able to create an encrypted S3 repo using the new Mavericks build.  Files are transferring across and are encrypted.
+"""]]
diff --git a/doc/bugs/OSX_.dmg_unnecessarily_large_and_not_inherently_compressed.mdwn b/doc/bugs/OSX_.dmg_unnecessarily_large_and_not_inherently_compressed.mdwn
new file mode 100644
index 000000000..bf74aebe6
--- /dev/null
+++ b/doc/bugs/OSX_.dmg_unnecessarily_large_and_not_inherently_compressed.mdwn
@@ -0,0 +1,68 @@
+### Please describe the problem.
+
+The .dmg the OSX build is distributed in  is unnecessarily large (fixed size) and is externally compressed.
+
+I did a quick survey of .dmg images used for distributing other pieces of software which I had downloaded to my Mac, and most of them seem to be the UDBZ or the (older) UDZO formats which are internally compressed with bzip2 or zlib.  According to "man hdiutil", the UDBZ format is supported since 10.4 (Tiger).
+
+Below are a pair of patches: first to enable "make clean" to work on OSX, second to build the .dmg in the UDBZ format and without an explicit size (it seems to infer a correct size).  When I tested building it, it results in a .dmg which is slightly smaller than the old .dmg.bz2
+
+(This will also require a change to remove the .bz2 from the download links elsewhere in the wiki.)
+
+<pre>
+From 251e23bbe66cc63e98089554f91b2528a097e818 Mon Sep 17 00:00:00 2001
+From: Mike Magin <git@mike.magin.org>
+Date: Sun, 17 Nov 2013 08:11:05 -0800
+Subject: [PATCH 1/2] Add explicit path to find invocation in "make clean" target.
+
+---
+ Makefile | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 3f3ed35..5a0cebb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -83,8 +83,8 @@ clean:
+ 		Setup Build/InstallDesktopFile Build/EvilSplicer \
+ 		Build/Standalone Build/OSXMkLibs \
+ 		git-union-merge git-recover-repository
+-	find -name \*.o -exec rm {} \;
+-	find -name \*.hi -exec rm {} \;
++	find . -name \*.o -exec rm {} \;
++	find . -name \*.hi -exec rm {} \;
+ 
+ Build/InstallDesktopFile: Build/InstallDesktopFile.hs
+ 	$(GHC) --make $@
+-- 
+1.8.4.3
+
+From e66f767893b5ef70cbf69d420cb589071f88c784 Mon Sep 17 00:00:00 2001
+From: Mike Magin <git@mike.magin.org>
+Date: Sun, 17 Nov 2013 08:40:07 -0800
+Subject: [PATCH 2/2] Change .dmg build to include compression and not be fixed size.
+
+---
+ Makefile | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 5a0cebb..b6ac549 100644
+--- a/Makefile
++++ b/Makefile
+@@ -162,10 +162,9 @@ osxapp: Build/Standalone Build/OSXMkLibs
+ 
+ 	./Build/OSXMkLibs $(OSXAPP_BASE)
+ 	rm -f tmp/git-annex.dmg
+-	hdiutil create -size 640m -format UDRW -srcfolder tmp/build-dmg \
++	hdiutil create -format UDBZ -srcfolder tmp/build-dmg \
+ 		-volname git-annex -o tmp/git-annex.dmg
+ 	rm -f tmp/git-annex.dmg.bz2
+-	bzip2 --fast tmp/git-annex.dmg
+ 
+ ANDROID_FLAGS?=-f-XMPP
+ # Cross compile for Android.
+-- 
+1.8.4.3
+</pre>
+
+> Ah, that never seemed optimal. [[done]] --[[Joey]]
diff --git a/doc/bugs/Selfsigned_certificates_with_jabber_fail_miserably./comment_3_1e7578dd1321f399b12197056495b0b6._comment b/doc/bugs/Selfsigned_certificates_with_jabber_fail_miserably./comment_3_1e7578dd1321f399b12197056495b0b6._comment
new file mode 100644
index 000000000..62d723c7b
--- /dev/null
+++ b/doc/bugs/Selfsigned_certificates_with_jabber_fail_miserably./comment_3_1e7578dd1321f399b12197056495b0b6._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://launchpad.net/~psycojoker"
+ nickname="psycojoker"
+ subject="comment 3"
+ date="2013-11-25T09:54:33Z"
+ content="""
+Just to confirm that I'm also affected. Maybe you should add the possibility in the error message next to \"is the password correct?\".
+"""]]
diff --git a/doc/bugs/The_restricted_ssh_key_pair_makes_password_login___40__nearly__41___impossible/comment_20_b685050ee6fbb1a685e33f9656a10e84._comment b/doc/bugs/The_restricted_ssh_key_pair_makes_password_login___40__nearly__41___impossible/comment_20_b685050ee6fbb1a685e33f9656a10e84._comment
index 0ef43779b..83ab46051 100644
--- a/doc/bugs/The_restricted_ssh_key_pair_makes_password_login___40__nearly__41___impossible/comment_20_b685050ee6fbb1a685e33f9656a10e84._comment
+++ b/doc/bugs/The_restricted_ssh_key_pair_makes_password_login___40__nearly__41___impossible/comment_20_b685050ee6fbb1a685e33f9656a10e84._comment
@@ -4,5 +4,5 @@
  subject="comment 20"
  date="2013-04-14T20:59:26Z"
  content="""
-Ok, I don't know how gnome-keyring communicates with ssh, but that's good enough evidence for me: It was certianly gnome-keyring that got us into this mess!
+Ok, I don't know how gnome-keyring communicates with ssh, but that's good enough evidence for me: It was certainly gnome-keyring that got us into this mess!
 """]]
diff --git a/doc/bugs/Too_many_open_files.mdwn b/doc/bugs/Too_many_open_files.mdwn
new file mode 100644
index 000000000..3bb53e74d
--- /dev/null
+++ b/doc/bugs/Too_many_open_files.mdwn
@@ -0,0 +1,55 @@
+### Please describe the problem.
+
+The transferrer crashes after a while due to too many open files
+
+### What steps will reproduce the problem?
+
+Have a huge annex. Connect two local machines, one with the huge annex, the other one without. Let them copy files…
+
+### What version of git-annex are you using? On what operating system?
+
+latest version
+git-annex version: 5.20131117-gbd514dc
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi TDFA CryptoHash
+key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+
+on Mac OS X 10.9
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+[2013-11-22 10:49:19 CET] Transferrer: Downloaded oktaeder.png
+[2013-11-22 10:49:19 CET] Transferrer: Downloaded oktaeder.png
+[2013-11-22 10:49:19 CET] Transferrer: Downloaded oktaeder.png
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded klett-cover-neu.jpg
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded klett-cover-neu.jpg
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded kara-worl..ditor.gif
+git-annex: runInteractiveProcess: pipe: Too many open files
+Committer crashed: lsof: createProcess: resource exhausted (Too many open files)
+[2013-11-22 10:49:20 CET] Committer: warning Committer crashed: lsof: createProcess: resource exhausted (Too many open files)
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded kara-worl..ditor.gif
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded kara-worl..ditor.gif
+[2013-11-22 10:49:20 CET] Transferrer: Downloaded image1.png
+[2013-11-22 10:49:21 CET] Transferrer: Downloaded image1.png
+[2013-11-22 10:49:21 CET] Transferrer: Downloaded image.png
+[2013-11-22 10:49:21 CET] Transferrer: Downloaded image.png
+[2013-11-22 10:49:21 CET] Transferrer: Downloaded ikoseder.png
+[2013-11-22 10:49:21 CET] Transferrer: Downloaded ikoseder.png
+[2013-11-22 10:49:22 CET] Transferrer: Downloaded ikoseder.png
+[2013-11-22 10:49:22 CET] Transferrer: Downloaded ikosaeder.jpg
+git-annex: runInteractiveProcess: pipe: Too many open files
+ok
+(Recording state in git...)
+git-annex: socket: resource exhausted (Too many open files)
+[2013-11-22 10:49:22 CET] Transferrer: Downloaded ikosaeder.jpg
+Transferrer crashed: getCurrentDirectory: resource exhausted (Too many open files)
+[2013-11-22 10:49:22 CET] Transferrer: warning Transferrer crashed: getCurrentDirectory: resource exhausted (Too many open files)
+git-annex: runInteractiveProcess: pipe: Too many open files
+git-annex: runInteractiveProcess: pipe: Too many open files
+
+# End of transcript or log.
+"""]]
diff --git a/doc/bugs/Too_many_open_files/comment_1_d5d509b9b431d2ea6000ebc0aed62857._comment b/doc/bugs/Too_many_open_files/comment_1_d5d509b9b431d2ea6000ebc0aed62857._comment
new file mode 100644
index 000000000..477192692
--- /dev/null
+++ b/doc/bugs/Too_many_open_files/comment_1_d5d509b9b431d2ea6000ebc0aed62857._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T16:28:25Z"
+ content="""
+You can use `lsof -c git-annex` to find out what files git-annex has open. (lsof is included in the git-annex.app bundle on OSX) That would be very helpful in tracking this down.
+"""]]
diff --git a/doc/bugs/Transfers_continue_after_daemon_stopped.mdwn b/doc/bugs/Transfers_continue_after_daemon_stopped.mdwn
new file mode 100644
index 000000000..0d9b4f648
--- /dev/null
+++ b/doc/bugs/Transfers_continue_after_daemon_stopped.mdwn
@@ -0,0 +1,5 @@
+After creating a new pairing, I stopped the daemon through the webapp while it was syncing.  The webapp shut down and was no longer accessible, but git-annex continued running in the background, along with git-annex-shell, and they continued to run new transfers with new rsync processes.  This continued until I killed them all.
+
+I expected that when I stopped the daemon in the webapp, all git-annex processes and all transfers would stop.
+
+Using the 20131101 tarball.
diff --git a/doc/bugs/Transfers_continue_after_daemon_stopped/comment_1_39eb527d64367e6762281246f1d49b1f._comment b/doc/bugs/Transfers_continue_after_daemon_stopped/comment_1_39eb527d64367e6762281246f1d49b1f._comment
new file mode 100644
index 000000000..9d504f743
--- /dev/null
+++ b/doc/bugs/Transfers_continue_after_daemon_stopped/comment_1_39eb527d64367e6762281246f1d49b1f._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-05T16:01:14Z"
+ content="""
+I've checked, and shutting down the daemon does cause it to stop any transfers it is running.
+
+However, this does not stop other transfers initiated by the other paired computer.
+
+I'm ambivilant about whether local pairing should only allow transfers when both daemons are running.
+"""]]
diff --git a/doc/bugs/Tries_to_upload_to_remote_although_remote_is_dead/comment_3_0a785b5dfbf4eef30854d6bedb12b7d1._comment b/doc/bugs/Tries_to_upload_to_remote_although_remote_is_dead/comment_3_0a785b5dfbf4eef30854d6bedb12b7d1._comment
index 4eeedcd6b..e839e7a15 100644
--- a/doc/bugs/Tries_to_upload_to_remote_although_remote_is_dead/comment_3_0a785b5dfbf4eef30854d6bedb12b7d1._comment
+++ b/doc/bugs/Tries_to_upload_to_remote_although_remote_is_dead/comment_3_0a785b5dfbf4eef30854d6bedb12b7d1._comment
@@ -4,7 +4,7 @@
  subject="comment 3"
  date="2012-11-13T18:00:42Z"
  content="""
-I've tried & failed to reproduce this using the assistant. When I mark a repo as dead, and go into Configuration -> Manage repositories, the repository is not shown in the list of repositories it'll sync to, and it certianly doesn't upload any files to it.
+I've tried & failed to reproduce this using the assistant. When I mark a repo as dead, and go into Configuration -> Manage repositories, the repository is not shown in the list of repositories it'll sync to, and it certainly doesn't upload any files to it.
 
 
 """]]
diff --git a/doc/bugs/Truncated_file_transferred_via_S3/comment_1_5962358e6067448f633cc0eaf42f9ca7._comment b/doc/bugs/Truncated_file_transferred_via_S3/comment_1_5962358e6067448f633cc0eaf42f9ca7._comment
index 6a05b9750..f3583d31b 100644
--- a/doc/bugs/Truncated_file_transferred_via_S3/comment_1_5962358e6067448f633cc0eaf42f9ca7._comment
+++ b/doc/bugs/Truncated_file_transferred_via_S3/comment_1_5962358e6067448f633cc0eaf42f9ca7._comment
@@ -6,5 +6,5 @@
  content="""
 Did you get a chance to run `git annex fsck` on the file? I'd hope it would detect this problem.
 
-It's certianly possible for data to get corrupted somehow in transit. git-annex does not check that it got the expected contents until a fsck happens.
+It's certainly possible for data to get corrupted somehow in transit. git-annex does not check that it got the expected contents until a fsck happens.
 """]]
diff --git a/doc/bugs/Unnecessary_remote_transfers.mdwn b/doc/bugs/Unnecessary_remote_transfers.mdwn
new file mode 100644
index 000000000..9ae23e5a0
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers.mdwn
@@ -0,0 +1,24 @@
+### Please describe the problem.
+This is related to [[http://git-annex.branchable.com/bugs/assistant_does_not_always_use_repo_cost_info_when_queueing_downloads/]]
+
+### What steps will reproduce the problem?
+1.  Make a client repo on two machines on the local network.
+2.  Pair them.
+3.  Make a remote transfer repo.
+4.  Set up Jabber on both local machines.
+5.  Put a large file into the annex on one of the local machines.
+6.  Watch as the source client repo copies the file directly to the local paired machine, but also copies it to the remote transfer repo.
+7.  Wait for the local paired transfer to finish.
+8.  Manually disable syncing to the remote transfer repo.
+9.  Manually reenable it.
+10.  Watch as the remote transfer is not resumed.
+
+### What version of git-annex are you using? On what operating system?
+Using the 1 Nov Linux tarball, Ubuntu Raring.
+
+### Please provide any additional information below.
+This is a problem because unless I manually disable the remote repo, it will continue uploading the large file until it finishes, which uses the limited upstream bandwidth on my Internet connection--and this could take hours depending on the size of the file.
+
+The remote transfer wasn't even necessary to begin with, because it already had a direct connection to the local paired repo.  But even so, it should at least abort the remote transfer when the local transfer finishes.
+
+Thanks for your work on git-annex assistant.
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_10_b778fbb1386f0f51bf057ffacd590ebb._comment b/doc/bugs/Unnecessary_remote_transfers/comment_10_b778fbb1386f0f51bf057ffacd590ebb._comment
new file mode 100644
index 000000000..8c985243a
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_10_b778fbb1386f0f51bf057ffacd590ebb._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 10"
+ date="2013-11-03T02:19:04Z"
+ content="""
+Thanks, Joey.  I didn't realize that there were two instances of the assistant running.
+
+Forgive my ignorance, but if I disable the assistant running in the backup repo, will the other assistant still backup files to it?
+
+Also, from a UI perspective, does the webapp currently not seem to support secondary internal drives, at least in a useful way?
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_11_55430eac842d0a192dc7f41d7730e4d5._comment b/doc/bugs/Unnecessary_remote_transfers/comment_11_55430eac842d0a192dc7f41d7730e4d5._comment
new file mode 100644
index 000000000..808c5bca6
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_11_55430eac842d0a192dc7f41d7730e4d5._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 11"
+ date="2013-11-03T02:32:47Z"
+ content="""
+Yes, either of the assistants will still back up files to it, as long as they have it configured as a git remote. The same way that your transfer repository is (probably) not running the git-annex assistant.
+
+It does sound like using the removable drive UI would have saved you some trouble. I'm not sure why the webapp would not list a llvm device as a removable drive -- from inspecting the code, it seems like it would not be filtered out, as long as /proc/mounts shows the decive as /dev/something (I don't have a llvm device handy to check what it looks like).
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_1_00c18e07678dc513a02d974fe059df73._comment b/doc/bugs/Unnecessary_remote_transfers/comment_1_00c18e07678dc513a02d974fe059df73._comment
new file mode 100644
index 000000000..7baa58489
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_1_00c18e07678dc513a02d974fe059df73._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-02T19:54:44Z"
+ content="""
+In what order does the webapp list your repositories? 
+
+When a new file appears, it will always go through the list of repositories in order, and try to transfer the file to each in turn, unless the configuration indicates it shouldn't. So, if the remote transfer repo is listed before the local repo, it will first upload the file to the transfer repo, and then upload it to the local repo. (And then later on, remove it from the transfer repo, since the file has reached all clients, probably.) OTOH, if the local repo comes first, it will upload the file to it over the LAN, and then when it comes to the transfer repo, if the file has successfully been sent to all clients, the transfer repo will no longer want it, and so no expensive upload is done over the internet.
+
+You can re-order the repository list in the webapp by dragging them up and down. It should default to having your locally paired repos first, unless you've changed it. If you think it came up with the wrong order, paste in your .git/config before you re-order the repositories..
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_2_2e9992dbfceabd6df535a2770626de16._comment b/doc/bugs/Unnecessary_remote_transfers/comment_2_2e9992dbfceabd6df535a2770626de16._comment
new file mode 100644
index 000000000..cc0cb067e
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_2_2e9992dbfceabd6df535a2770626de16._comment
@@ -0,0 +1,35 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 2"
+ date="2013-11-02T22:48:18Z"
+ content="""
+The webapp has the remote repo at the bottom of the list.  But here's .git/config.  It has a high repo cost for the local paired repo, and no cost listed for the remote one:
+
+[[!format sh \"\"\"
+[core]
+        repositoryformatversion = 0
+        filemode = true
+        bare = false
+        logallrefupdates = true
+[annex]
+        uuid = 946f9095-588b-4421-b66a-4a1e5632ff6b
+        version = 3
+        direct = true
+        diskreserve = 1 megabyte
+        numcopies = 1
+        debug = false
+[gc]
+        auto = 0
+[remote \"Onyx\"]
+        url = ssh://me@git-annex-Onyx.local-me_annex/~/annex/
+        annex-uuid = 80709bc2-3cbe-434b-b7b9-306278b9a4e9
+        annex-cost = 125.0
+        fetch = +refs/heads/*:refs/remotes/Onyx/*
+[remote \"Remote\"]
+        annex-rsyncurl = username@git-annex-example.net-username_annex:annex/
+        annex-uuid = 33930bae-63d2-4a52-b330-58872aaeb1bf
+        fetch = 
+        annex-sync = true
+\"\"\"]]
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_3_a98f3091a6a658919f0562cf396439c2._comment b/doc/bugs/Unnecessary_remote_transfers/comment_3_a98f3091a6a658919f0562cf396439c2._comment
new file mode 100644
index 000000000..b6900f339
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_3_a98f3091a6a658919f0562cf396439c2._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 3"
+ date="2013-11-02T22:59:18Z"
+ content="""
+Also, I just realized that it's uploading two large files to my remote transfer repo, even though I already have both files in my local paired repo on both systems; i.e. there's no need to send it to the transfer repo at all.  And it was yesterday when the two files were transferred.  So I have no idea why today it thinks it needs to upload them to the transfer repo.  :/
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_4_417c1e8e27ee1a1f9ebf9160560605c5._comment b/doc/bugs/Unnecessary_remote_transfers/comment_4_417c1e8e27ee1a1f9ebf9160560605c5._comment
new file mode 100644
index 000000000..b0d4c1146
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_4_417c1e8e27ee1a1f9ebf9160560605c5._comment
@@ -0,0 +1,96 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="Super confused"
+ date="2013-11-02T23:30:41Z"
+ content="""
+I think now I'm double- or triple-confused.  Here is me@desktop:~/annex/.git/config:
+
+[[!format sh \"\"\"
+[core]
+        repositoryformatversion = 0
+        filemode = true
+        bare = false
+        logallrefupdates = true
+[annex]
+        uuid = 80709bc2-3cbe-434b-b7b9-306278b9a4e9
+        version = 3
+        direct = true
+        fscknudge = true
+[gc]
+        auto = 0
+[remote \"laptop\"]
+        url = ssh://me@git-annex-laptop-me_annex/~/annex/
+        annex-uuid = 946f9095-588b-4421-b66a-4a1e5632ff6b
+        annex-cost = 175.0
+        fetch = +refs/heads/*:refs/remotes/laptop/*
+[remote \"Remote\"]
+        annex-rsyncurl = username@example.net:annex/
+        annex-uuid = 33930bae-63d2-4a52-b330-58872aaeb1bf
+        fetch = 
+        annex-sync = false
+[remote \"backupOndesktop\"]
+        url = /mnt/debian/home/me/annex-backup
+        annex-uuid = 86535965-6ca7-4bf3-89af-bca3a07f96f9
+        fetch = +refs/heads/*:refs/remotes/backupOndesktop/*
+\"\"\"]]
+
+What I have set up (or intended to set up) is:
+
+* Client: me@laptop:~/annex
+* Client: me@desktop:~/annex
+* Transfer: username@example.net:~/annex
+* Full Backup: me@desktop:/mnt/debian/home/me/annex-backup
+
+What I expected was that:
+
+1.  The two Client repos would sync directly over the LAN whenever possible.
+2.  The transfer repo would be used only to sync the laptop and desktop, and then only if my laptop were not on the LAN with my desktop.
+3.  The Full Backup repo would be synced directly with the me@desktop Client repo, within the same system, from one hard disk to the other.
+
+But what I'm seeing is...not quite that.
+
+1.  It's very confusing (to me, at least) that on my desktop system I can look at my annex setup from the \"perspective\" of both local repos.  When I \"switch\" to the other repo, the setup looks different: even the same repos can have different names and descriptions, and can be enabled and disabled independently depending on the \"perspective\"...but their Type is still the same.
+
+2.  Looking from the \"perspective\" of the Full Backup repo, I'm seeing files being transferred to the Transfer repo, even though those files are already present in both Client repos, and even though the webapp says that the Full Backup repo has been synced.  When I disable and reenable the Transfer repo, it starts those transfers over again, even though they aren't necessary.  For example, here is the log from disabling and reenabling the Transfer repo from the \"perspective\" of the Full Backup repo:
+
+[[!format sh \"\"\"
+[2013-11-02 18:24:35 CDT] main: Syncing with example.net_annex 
+(gpg) 
+gpg: Terminated caught ... exiting
+[2013-11-02 18:24:49 CDT] call: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"config\",\"remote.example.net_annex.annex-sync\",\"true\"]
+[2013-11-02 18:24:49 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:49 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:49 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:49 CDT] main: Syncing with example.net_annex 
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"symbolic-ref\",\"HEAD\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"refs/heads/master\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"git-annex\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"log\",\"refs/heads/git-annex..2c42d607c099b6ec4a20603b809f44d161e42489\",\"--oneline\",\"-n1\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"symbolic-ref\",\"HEAD\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"refs/heads/master\"]
+[2013-11-02 18:24:49 CDT] TransferScanner: starting scan of [Remote { name =\"example.net_annex\" }]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"ls-files\",\"--cached\",\"-z\",\"--\"]
+[2013-11-02 18:24:49 CDT] TransferScanner: queued Upload UUID \"33930bae-63d2-4a52-b330-58872aaeb1bf\" video.flv Nothing : expensive scan found missing object
+[2013-11-02 18:24:49 CDT] Transferrer: Transferring: Upload UUID \"33930bae-63d2-4a52-b330-58872aaeb1bf\" video.flv Nothing
+[2013-11-02 18:24:49 CDT] TransferScanner: queued Upload UUID \"33930bae-63d2-4a52-b330-58872aaeb1bf\" image.jpg Nothing : expensive scan found missing object
+[2013-11-02 18:24:49 CDT] call: /home/me/.bin/git-annex.linux/git-annex [\"transferkeys\",\"--readfd\",\"35\",\"--writefd\",\"34\"]
+[2013-11-02 18:24:49 CDT] TransferScanner: queued Upload UUID \"33930bae-63d2-4a52-b330-58872aaeb1bf\" linux-image-3.8.0-29-generic_3.8.0-29.42_i386.deb Nothing : expensive scan found missing object
+[2013-11-02 18:24:49 CDT] TransferScanner: finished scan of [Remote { name =\"example.net_annex\" }]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"git-annex\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
+[2013-11-02 18:24:49 CDT] read: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"log\",\"refs/heads/git-annex..2c42d607c099b6ec4a20603b809f44d161e42489\",\"--oneline\",\"-n1\"]
+[2013-11-02 18:24:49 CDT] chat: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"cat-file\",\"--batch\"]
+[2013-11-02 18:24:49 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:49 CDT] TransferWatcher: transfer starting: Upload UUID \"33930bae-63d2-4a52-b330-58872aaeb1bf\" video.flv Nothing
+(gpg) [2013-11-02 18:24:49 CDT] chat: gpg [\"--batch\",\"--no-tty\",\"--use-agent\",\"--quiet\",\"--trust-model\",\"always\",\"--batch\",\"--passphrase-fd\",\"20\",\"--symmetric\",\"--force-mdc\",\"--no-textmode\"]
+[2013-11-02 18:24:50 CDT] call: git [\"--git-dir=/mnt/debian/home/me/annex-backup/.git\",\"--work-tree=/mnt/debian/home/me/annex-backup\",\"config\",\"remote.example.net_annex.annex-sync\",\"false\"]
+[2013-11-02 18:24:50 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:50 CDT] read: git [\"config\",\"--null\",\"--list\"]
+[2013-11-02 18:24:50 CDT] read: git [\"config\",\"--null\",\"--list\"]
+
+gpg: Terminated caught ... exiting\"\"\"]]
+
+I have no idea why it's doing that, because all three of those files are already in both Client repos and the Full Backup repo.
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_5_eb5a2717a1f0c7bb761d2a7866b23def._comment b/doc/bugs/Unnecessary_remote_transfers/comment_5_eb5a2717a1f0c7bb761d2a7866b23def._comment
new file mode 100644
index 000000000..0e2ec4ec8
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_5_eb5a2717a1f0c7bb761d2a7866b23def._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="Deleting repos from different perspectives"
+ date="2013-11-02T23:33:48Z"
+ content="""
+One other thing, sorry, but I think this is important:  From the perspective of the Full Backup repo, I set the Transfer repo to be deleted, thinking that would prevent the desktop's Client and Full Backup repos from syncing through the Transfer repo.  But then when I switch to the perspective of the desktop's Client repo, it is \"cleaning out\" the Transfer repo--but I wanted the Transfer repo to be used for syncing the two Client repos!  So I set it back to Transfer instead of Unwanted...but then when I switch back to the Full Backup perspective, the Transfer repo is no longer Unwanted.
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_6_89f756db1f3f2e60a3bd1f35f55fee43._comment b/doc/bugs/Unnecessary_remote_transfers/comment_6_89f756db1f3f2e60a3bd1f35f55fee43._comment
new file mode 100644
index 000000000..509cc3f3f
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_6_89f756db1f3f2e60a3bd1f35f55fee43._comment
@@ -0,0 +1,40 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="config from backup repo"
+ date="2013-11-03T00:20:11Z"
+ content="""
+Sorry for posting over and over again, just trying to provide info when I discover it.
+
+Here's **/mnt/debian/home/me/annex-backup/.git/config**
+
+[[!format sh \"\"\"
+[core]
+        repositoryformatversion = 0
+        filemode = true
+        bare = false
+        logallrefupdates = true
+[annex]
+        uuid = 86535965-6ca7-4bf3-89af-bca3a07f96f9
+        version = 3
+        direct = true
+        fscknudge = true
+        diskreserve = 100 megabyte
+        numcopies = 1
+        debug = false
+[gc]
+        auto = 0
+[remote \"desktop\"]
+        url = /home/me/annex
+        fetch = +refs/heads/*:refs/remotes/desktop/*
+        annex-uuid = 80709bc2-3cbe-434b-b7b9-306278b9a4e9
+[remote \"Remote\"]
+        annex-rsyncurl = username@example.net:annex/
+        annex-uuid = 33930bae-63d2-4a52-b330-58872aaeb1bf
+        annex-sync = false
+        fetch =\"\"\"]]
+
+1.  Should I remove the \"Remote\" Transfer repo from this config file to prevent it from using the Transfer repo?  I only want this repo to sync directly with the other internal hard disk.
+
+2.  Is it correct for git-annex to add this Transfer repo to this config file in the first place?
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_7_5aaf8766a7ba05c4f92715e5d5175a8f._comment b/doc/bugs/Unnecessary_remote_transfers/comment_7_5aaf8766a7ba05c4f92715e5d5175a8f._comment
new file mode 100644
index 000000000..f117f15c1
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_7_5aaf8766a7ba05c4f92715e5d5175a8f._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 7"
+ date="2013-11-03T00:45:09Z"
+ content="""
+* The costs you show look fine.
+* Yes, deleting a repository in the webapp actually deletes it. It doesn't just remove the remote from .git/config. Most people using the webapp don't want to draw such a fine distinction, I think.
+* It's not a very usual configuration to have 2 repositories on the same machine with the git-annex assistant running in both. You might just want to configure the assistant to not run in the backup repository.
+
+Some of the things you've said suggest that the backup repository might not be immediately noticing when changes are pushed to it. Since its location is shown as /mnt/debian/home/me, I have to wonder if that's some NFS mount or other network filesystem causing problems.
+
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_8_e856b350632cc865d16d1995a6cdf065._comment b/doc/bugs/Unnecessary_remote_transfers/comment_8_e856b350632cc865d16d1995a6cdf065._comment
new file mode 100644
index 000000000..1177205e3
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_8_e856b350632cc865d16d1995a6cdf065._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 8"
+ date="2013-11-03T01:07:31Z"
+ content="""
+> It's not a very usual configuration to have 2 repositories on the same machine with the git-annex assistant running in both. You might just want to configure the assistant to not run in the backup repository.
+
+Maybe that's the crux of the problem.  But I'm not sure what I did wrong to make that happen.  I have a second internal hard disk in my desktop system, and I wanted to put a Full Backup repo on it.  I tried to add a \"Removable drive\" repo (since I sometimes unplug it to swap cables with a DVD drive), but since the assistant didn't detect any actual removable drives, that didn't work.  So I used \"Add another repository\" and set it to a Full Backup repo.  Is that the wrong way to do it?  :)
+
+> Some of the things you've said suggest that the backup repository might not be immediately noticing when changes are pushed to it. Since its location is shown as /mnt/debian/home/me, I have to wonder if that's some NFS mount or other network filesystem causing problems.
+
+/mnt/debian is /dev/mapper/lvm-root, another internal disk.  The disk is working fine.  :)
+"""]]
diff --git a/doc/bugs/Unnecessary_remote_transfers/comment_9_64f831545b34b78452952cf49b5f5b05._comment b/doc/bugs/Unnecessary_remote_transfers/comment_9_64f831545b34b78452952cf49b5f5b05._comment
new file mode 100644
index 000000000..03127c4ad
--- /dev/null
+++ b/doc/bugs/Unnecessary_remote_transfers/comment_9_64f831545b34b78452952cf49b5f5b05._comment
@@ -0,0 +1,25 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 9"
+ date="2013-11-03T01:52:56Z"
+ content="""
+Ok, since we don't have NFS craziness, I'm going to put theories about it not noticing incoming syncs on hold. (I think I probably misunderstood [this comment](http://git-annex.branchable.com/bugs/Unnecessary_remote_transfers/#comment-39490c318620c141e7557b7bcba0e5c8) and anyway the assistant has some throttling so won't always immediately load config changes that have been synced to it if some other config changes were loaded a minute before.)
+
+I think this behavior can probably be explained without resorting to any bugs, now that I have, I think, a full picture of the repository network:
+
+<pre>
+laptop <-> desktop <-> backup
+    |         |       |
+    v         v       v
+      transfer (cloud)
+</pre>
+
+Now when a file is added to desktop, it immediately copies it to backup, which is on the same machine, so that happens quite quickly. Then it starts sending it across the LAN to laptop.
+
+Meanwhile, the assistant daemon running on backup wakes up, notices it's just received an object, and sees that this object is currently located on only desktop and backup, but not yet on laptop or transfer. Which means that it should send the object to transfer, from which it will eventually reach laptop.
+
+The only ways I can think of to avoid such an unnecessary transfer would be a) for desktop could somehow tell backup that it's in the process of sending the file to laptop or b) for a map of current state of the network to be constructed and maintained and analyzed automatically, so it it could conclude backup does not need to send files to transfer if they're already present on desktop. There is some discussion about this in [[design/assistant/syncing]]. Hard problem in general I think, although slightly less hard in this specific case since desktop and backup know they're in the same machine.
+
+But it should be easy to configure it so this doesn't happen. Just make backup not have the transfer repository configured as a remote (or just pause it syncing to there in the webapp). Or, don't run the assistant at all on backup (see `~/.config/git-annex/autostart`).
+"""]]
diff --git a/doc/bugs/Watcher_crashed_in_Android_on___47__storage__47__sdcard1_-_bug__63__/comment_3_1a7542249b9c37507126e97441057c12._comment b/doc/bugs/Watcher_crashed_in_Android_on___47__storage__47__sdcard1_-_bug__63__/comment_3_1a7542249b9c37507126e97441057c12._comment
new file mode 100644
index 000000000..9bc0c90e6
--- /dev/null
+++ b/doc/bugs/Watcher_crashed_in_Android_on___47__storage__47__sdcard1_-_bug__63__/comment_3_1a7542249b9c37507126e97441057c12._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 3"
+ date="2013-11-10T18:18:09Z"
+ content="""
+Seems to me this was probably fixed in [[!commit 6b37fcffd872b62fb78047a77e4cee5ab0bb57f1]].
+
+However, I don't know why permission problems would happen on Android, which typically uses a filesystem that does not have restricted permissions for the sdcard.
+
+If you upgrade, you should be able to see if it fixed the crash, and it will also mention any file or directory that it's unable to read in the log.
+"""]]
diff --git a/doc/bugs/With_S3__44___GPG_ask_for_a_new_passphrase/comment_2_e5d42b623017acedf6a3890ce15680a3._comment b/doc/bugs/With_S3__44___GPG_ask_for_a_new_passphrase/comment_2_e5d42b623017acedf6a3890ce15680a3._comment
index d742bbe58..7b26ca738 100644
--- a/doc/bugs/With_S3__44___GPG_ask_for_a_new_passphrase/comment_2_e5d42b623017acedf6a3890ce15680a3._comment
+++ b/doc/bugs/With_S3__44___GPG_ask_for_a_new_passphrase/comment_2_e5d42b623017acedf6a3890ce15680a3._comment
@@ -4,7 +4,7 @@
  subject="comment 2"
  date="2013-01-16T02:17:26Z"
  content="""
-Someone else reported what sounds like the same bug at [[encryption_given_a_gpg_keyid_still_uses_symmetric_encryption]]. It sounds like this is somehow an agent bug. I cannot reproduce it. I can hypothesise that, if this bug is occurring, you'll be prompted for a passphrase when running this command.. which if it happens would certianly be a bug in gpg or its agent
+Someone else reported what sounds like the same bug at [[encryption_given_a_gpg_keyid_still_uses_symmetric_encryption]]. It sounds like this is somehow an agent bug. I cannot reproduce it. I can hypothesise that, if this bug is occurring, you'll be prompted for a passphrase when running this command.. which if it happens would certainly be a bug in gpg or its agent
 
 touch foo; echo foo| gpg --symmetric --passphrase-fd=0 foo
 
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes.mdwn b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes.mdwn
new file mode 100644
index 000000000..e7ff53723
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes.mdwn
@@ -0,0 +1,44 @@
+### Please describe the problem.
+git-annex assistant is currently running.  Here is the output of **ps -A u | grep -i git**:
+
+[[!format sh """
+5457 pts/2    Z+     0:00 [git-annex] <defunct>
+5510 ?        Sl     0:05 git-annex assistant
+5522 ?        S      0:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+5573 ?        S      0:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+5679 ?        SN     0:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex check-attr -z --stdin annex.backend annex.numcopies --
+5680 ?        Z      0:03 [git-annex] <defunct>
+5710 ?        Z      0:00 [git-annex] <defunct>
+5732 pts/2    Z+     0:00 [git-annex] <defunct>
+5752 pts/2    Z+     0:00 [git-annex] <defunct>
+5785 ?        Ss     0:00 ssh: .git/annex/ssh/example.net [mux]                                                                                                                                     
+5905 ?        Z      0:00 [git-annex] <defunct>
+5923 ?        Z      0:00 [git-annex] <defunct>
+6513 pts/2    Z+     0:00 [git-annex] <defunct>
+6552 ?        Z      0:00 [git-annex] <defunct>
+7797 ?        Z      0:00 [git-annex] <defunct>
+7873 pts/2    Z      0:00 [git-annex] <defunct>
+8708 pts/2    Z+     0:00 [git-annex] <defunct>
+9821 ?        Z      0:00 [git-annex] <defunct>
+9841 pts/2    Z+     0:00 [git-annex] <defunct>
+10462 ?        Z      0:00 [git-annex] <defunct>
+10522 pts/2    Z      0:00 [git-annex] <defunct>
+12777 pts/2    Z+     0:00 [git-annex] <defunct>
+13878 pts/2    Z+     0:00 [git-annex] <defunct>
+14254 ?        Z      0:00 [git-annex] <defunct>
+14276 pts/2    Z+     0:00 [git-annex] <defunct>
+15932 ?        Sl     0:00 git-annex transferkeys --readfd 37 --writefd 20
+16022 pts/2    Sl     0:00 git-annex transferkeys --readfd 28 --writefd 22
+16079 pts/2    S      0:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+16081 ?        S      0:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+31565 pts/2    Sl+    0:20 git-annex webapp
+31580 pts/2    S+     0:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31590 pts/2    S+     0:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31618 pts/2    S+     0:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31635 ?        Sl     9:26 /usr/lib/firefox/firefox /mnt/debian/home/me/annex-backup/.git/annex/webapp.html
+31689 pts/2    SN+    0:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup check-attr -z --stdin annex.backend annex.numcopies --
+31812 pts/2    Z      0:00 [git-annex] <defunct>
+31835 ?        Ss     0:02 ssh: .git/annex/ssh/example.net [mux]
+"""]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_1_0f8b248025722309e9577d7dad74b76b._comment b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_1_0f8b248025722309e9577d7dad74b76b._comment
new file mode 100644
index 000000000..578fecb58
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_1_0f8b248025722309e9577d7dad74b76b._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-03T01:12:25Z"
+ content="""
+This is apparently the same repository where [[all_this_went_on|bugs/Unnecessary_remote_transfers]].
+
+I don't know if this is indicative of a problem. I see more zombies than I would normally expect, but I don't know if the number is growing, or shrinking, or staying the same. You should at least look at ps -f to see which of the multiple git-annex assistant daemons you have configured to run on this machine (not a usual configuration) is the parent of the zombies.
+"""]]
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_2_f5f7db688a2a93ee7453674fb742043b._comment b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_2_f5f7db688a2a93ee7453674fb742043b._comment
new file mode 100644
index 000000000..ceb05ea0c
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_2_f5f7db688a2a93ee7453674fb742043b._comment
@@ -0,0 +1,52 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 2"
+ date="2013-11-03T01:19:42Z"
+ content="""
+Indeed.  I've been looking forward to setting up git-annex assistant for a long time, waiting until I had more free time, and was finally pushed to do it when I had a weird problem with Dropbox.  I'm not sure what I did wrong to make such a mess, haha.
+
+I see \"5510 git-annex assistant\" and \"31565 git-annex webapp\"--does the \"webapp\" one count as an assistant process too?
+[[!format sh \"\"\"$ ps -ef | gi git
+UID        PID  PPID  C STIME TTY          TIME CMD
+me        3404 31565  0 17:44 pts/2    00:00:04 [git-annex] <defunct>
+me        5457 31565  0 17:59 pts/2    00:00:00 [git-annex] <defunct>
+me        5510     1  0 17:59 ?        00:00:06 git-annex assistant
+me        5522  5510  0 17:59 ?        00:00:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+me        5573  5510  0 17:59 ?        00:00:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+me        5679  5510  0 17:59 ?        00:00:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex check-attr -z --stdin annex.backend annex.numcopies --
+me        5680  5510  0 17:59 ?        00:00:03 [git-annex] <defunct>
+me        5710  5510  0 18:00 ?        00:00:00 [git-annex] <defunct>
+me        5732 31565  0 18:00 pts/2    00:00:00 [git-annex] <defunct>
+me        5752 31565  0 18:00 pts/2    00:00:00 [git-annex] <defunct>
+me        5785     1  0 18:01 ?        00:00:00 ssh: .git/annex/ssh/example.net [mux]                                                                                                                                     
+me        5905  5510  0 18:02 ?        00:00:00 [git-annex] <defunct>
+me        5923  5510  0 18:02 ?        00:00:00 [git-annex] <defunct>
+me        6513 31565  0 18:05 pts/2    00:00:00 [git-annex] <defunct>
+me        6552  5510  0 18:06 ?        00:00:00 [git-annex] <defunct>
+me        7797  5510  0 18:09 ?        00:00:00 [git-annex] <defunct>
+me        7873 31565  0 18:09 pts/2    00:00:00 [git-annex] <defunct>
+me        8708 31565  0 18:10 pts/2    00:00:00 [git-annex] <defunct>
+me        9821  5510  0 18:12 ?        00:00:00 [git-annex] <defunct>
+me        9841 31565  0 18:14 pts/2    00:00:00 [git-annex] <defunct>
+me       10462  5510  0 18:23 ?        00:00:00 [git-annex] <defunct>
+me       10522 31565  0 18:24 pts/2    00:00:00 [git-annex] <defunct>
+me       12777 31565  0 18:34 pts/2    00:00:00 [git-annex] <defunct>
+me       13878 31565  0 18:35 pts/2    00:00:00 [git-annex] <defunct>
+me       14254  5510  0 18:36 ?        00:00:00 [git-annex] <defunct>
+me       14276 31565  0 18:36 pts/2    00:00:00 [git-annex] <defunct>
+me       15932  5510  0 18:55 ?        00:00:00 git-annex transferkeys --readfd 37 --writefd 20
+me       16022 31565  0 18:55 pts/2    00:00:00 git-annex transferkeys --readfd 28 --writefd 22
+me       16079 16022  0 18:55 pts/2    00:00:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+me       16081 15932  0 18:55 ?        00:00:00 git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+me       25136 25135  0 20:15 pts/6    00:00:00 grep -i git
+me       31565 31478  0 17:42 pts/2    00:00:21 git-annex webapp
+me       31580 31565  0 17:42 pts/2    00:00:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+me       31590 31565  0 17:42 pts/2    00:00:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+me       31618 31565  0 17:42 pts/2    00:00:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+me       31635 27578  8 17:42 ?        00:13:42 /usr/lib/firefox/firefox /mnt/debian/home/me/annex-backup/.git/annex/webapp.html
+me       31689 31565  0 17:42 pts/2    00:00:00 git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup check-attr -z --stdin annex.backend annex.numcopies --
+me       31812 31565  0 17:42 pts/2    00:00:00 [git-annex] <defunct>
+me       31835     1  0 17:42 ?        00:00:02 ssh: .git/annex/ssh/example.net [mux]\"\"\"]]
+
+"""]]
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_3_ffcae976aa3dc2426188797c1aaffb82._comment b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_3_ffcae976aa3dc2426188797c1aaffb82._comment
new file mode 100644
index 000000000..78e816f06
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_3_ffcae976aa3dc2426188797c1aaffb82._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-03T01:31:26Z"
+ content="""
+`ps fax` is much easier to read
+
+Yes, the assistant can be started by either `git annex assistant` or, if it's not already running, `git annex webapp`
+"""]]
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_4_8a7ff6841ad7c27ead06bf12f46b20a0._comment b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_4_8a7ff6841ad7c27ead06bf12f46b20a0._comment
new file mode 100644
index 000000000..2bf32bd37
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_4_8a7ff6841ad7c27ead06bf12f46b20a0._comment
@@ -0,0 +1,49 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 4"
+ date="2013-11-03T01:35:32Z"
+ content="""
+Ah, thank you.  I get lost in ps's man page.  :)
+
+[[!format sh \"\"\"
+31635 ?        Rl    16:16  \_ /usr/lib/firefox/firefox /mnt/debian/home/me/annex-backup/.git/annex/webapp.html
+31565 pts/2    Sl+    0:21  |       \_ git-annex webapp
+31580 pts/2    S+     0:00  |           \_ git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31590 pts/2    S+     0:00  |           \_ git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31618 pts/2    S+     0:00  |           \_ git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+31689 pts/2    SN+    0:00  |           \_ git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup check-attr -z --stdin annex.backend annex.numcopies --
+31812 pts/2    Z      0:00  |           \_ [git-annex] <defunct>
+ 3404 pts/2    Z      0:04  |           \_ [git-annex] <defunct>
+ 5457 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+ 5732 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+ 5752 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+ 6513 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+ 7873 pts/2    Z      0:00  |           \_ [git-annex] <defunct>
+ 8708 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+ 9841 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+10522 pts/2    Z      0:00  |           \_ [git-annex] <defunct>
+12777 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+13878 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+14276 pts/2    Z+     0:00  |           \_ [git-annex] <defunct>
+16022 pts/2    Sl     0:00  |           \_ git-annex transferkeys --readfd 28 --writefd 22
+16079 pts/2    S      0:00  |               \_ git --git-dir=/mnt/debian/home/me/annex-backup/.git --work-tree=/mnt/debian/home/me/annex-backup cat-file --batch
+26828 pts/6    S+     0:00  |       \_ grep -i git
+31835 ?        Ss     0:02 ssh: .git/annex/ssh/example.net [mux]                                                                                                                                     
+ 5510 ?        Sl     0:06 git-annex assistant
+ 5522 ?        S      0:00  \_ git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+ 5573 ?        S      0:00  \_ git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+ 5679 ?        SN     0:00  \_ git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex check-attr -z --stdin annex.backend annex.numcopies --
+ 5680 ?        Z      0:03  \_ [git-annex] <defunct>
+ 5710 ?        Z      0:00  \_ [git-annex] <defunct>
+ 5905 ?        Z      0:00  \_ [git-annex] <defunct>
+ 5923 ?        Z      0:00  \_ [git-annex] <defunct>
+ 6552 ?        Z      0:00  \_ [git-annex] <defunct>
+ 7797 ?        Z      0:00  \_ [git-annex] <defunct>
+ 9821 ?        Z      0:00  \_ [git-annex] <defunct>
+10462 ?        Z      0:00  \_ [git-annex] <defunct>
+14254 ?        Z      0:00  \_ [git-annex] <defunct>
+15932 ?        Sl     0:00  \_ git-annex transferkeys --readfd 37 --writefd 20
+16081 ?        S      0:00      \_ git --git-dir=/home/me/annex/.git --work-tree=/home/me/annex cat-file --batch
+ 5785 ?        Ss     0:00 ssh: .git/annex/ssh/example.net [mux]    \"\"\"]]
+"""]]
diff --git a/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_5_406fdee0728680774a69d28446163f10._comment b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_5_406fdee0728680774a69d28446163f10._comment
new file mode 100644
index 000000000..f8f223524
--- /dev/null
+++ b/doc/bugs/Zombie_processes_and__47__or_stuck_git_processes/comment_5_406fdee0728680774a69d28446163f10._comment
@@ -0,0 +1,26 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 5"
+ date="2013-11-03T02:33:14Z"
+ content="""
+I believe that these zombies were all caused by switching between repository views in the webapp. I was able to reproduce 1 zombie per switch between repos.
+
+There are a few other places where git-annex execs itself, but not many, and most of them are often used and it would be noticed if they were crypts from which pour forth the living dead. (Oddly the TV show I was thinking about watching this evening.)
+
+<pre>
+joey@darkstar:~/src/git-annex>git grep readProgramFile
+Assistant/Repair.hs:		program <- readProgramFile
+Assistant/Threads/Cronner.hs:	program <- liftIO $ readProgramFile
+Assistant/Threads/Cronner.hs:			program <- readProgramFile
+Assistant/Threads/Transferrer.hs:	program <- liftIO readProgramFile
+Assistant/TransferSlots.hs:		program <- liftIO readProgramFile
+Assistant/WebApp/Control.hs:		program <- readProgramFile
+Assistant/WebApp/OtherRepos.hs:	program <- readProgramFile
+Assistant/XMPP/Git.hs:		program <- readProgramFile
+Command/Assistant.hs:	program <- readProgramFile
+Config/Files.hs:readProgramFile :: IO FilePath
+Config/Files.hs:readProgramFile = do
+Remote/Git.hs:		program <- readProgramFile
+</pre>
+"""]]
diff --git a/doc/bugs/__34__Configuring_Jabber_Account__34___fails_with_a___34__Network_unreachable__34___error./comment_3_ed36f503f88611382b50687608b9b7e7._comment b/doc/bugs/__34__Configuring_Jabber_Account__34___fails_with_a___34__Network_unreachable__34___error./comment_3_ed36f503f88611382b50687608b9b7e7._comment
new file mode 100644
index 000000000..a69763af7
--- /dev/null
+++ b/doc/bugs/__34__Configuring_Jabber_Account__34___fails_with_a___34__Network_unreachable__34___error./comment_3_ed36f503f88611382b50687608b9b7e7._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 3"
+ date="2013-11-08T18:42:22Z"
+ content="""
+Seems like I should fix the standalone linux tarball to either include the host program, or better, build git-annex with the Haskell [DNS library](https://hackage.haskell.org/package/dns). (I think that the Mac app and other builds are built with DNS by default, since they have dependencies installed using cabal directly).
+
+I need to first get that library included in Debian, so I can install it reliably on my build systems.
+"""]]
diff --git a/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu.mdwn b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu.mdwn
new file mode 100644
index 000000000..7366e6ff2
--- /dev/null
+++ b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu.mdwn
@@ -0,0 +1,21 @@
+### Please describe the problem.
+
+quite often is desired to fetch/navigate through the git annex installation under git annex user, e.g. to fetch the log to be provided here for the "additional information".
+Given already big size of the app bundling some lightweight ssh server should not be a major size hit, but would ease troubleshooting and bug reporting
+
+### What steps will reproduce the problem?
+
+
+### What version of git-annex are you using? On what operating system?
+
+Android from Nov 18
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
diff --git a/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_1_9bb53c45d685b368c7ba1758885f2874._comment b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_1_9bb53c45d685b368c7ba1758885f2874._comment
new file mode 100644
index 000000000..36440eac5
--- /dev/null
+++ b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_1_9bb53c45d685b368c7ba1758885f2874._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T16:09:19Z"
+ content="""
+This was previously suggested in the forum: [[forum/Suggestion:_Put_ssh_server_back_into_android_version]]
+
+As said there, I feel that `adb` is a better option in these situations. Of course, the git-annex bundle already has a ssh client, so you can rsync files from it to other ssh servers too.
+
+Also, the bundle is too big, I don't want to make it any bigger.
+"""]]
diff --git a/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_2_251311a04f1a610e54ebe8e9b92de72e._comment b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_2_251311a04f1a610e54ebe8e9b92de72e._comment
new file mode 100644
index 000000000..48707e82b
--- /dev/null
+++ b/doc/bugs/__91__wishlistAndroid:_bundle_an_ssh_server___40__dropbear__63____41___and_add_an_option_to_start_it_easily_with_the_terminal_app_menu/comment_2_251311a04f1a610e54ebe8e9b92de72e._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="http://yarikoptic.myopenid.com/"
+ nickname="site-myopenid"
+ subject="comment 2"
+ date="2013-11-27T04:30:53Z"
+ content="""
+we just shrinked the bundle by 60MB so there could be some space for sshd.
+
+adb might indeed be more powerful but would require usb connection (right?) -- at times not convenient
+
+syncing via ssh from phone: that is what I was trying to avoid -- working in the shell on the phone -- it is possible but a bit \"inconvenient\"
+sshd could be ran on any unprivileged port while letting the user who starts it know the IP and the port, thus making it easy to connect.
+"""]]
diff --git a/doc/bugs/android:_high_CPU_usage__44___unclear_how_to_quit/comment_7_d38d6f40db4c9437764c7b2ddf36b5a9._comment b/doc/bugs/android:_high_CPU_usage__44___unclear_how_to_quit/comment_7_d38d6f40db4c9437764c7b2ddf36b5a9._comment
index 66a560191..819d31672 100644
--- a/doc/bugs/android:_high_CPU_usage__44___unclear_how_to_quit/comment_7_d38d6f40db4c9437764c7b2ddf36b5a9._comment
+++ b/doc/bugs/android:_high_CPU_usage__44___unclear_how_to_quit/comment_7_d38d6f40db4c9437764c7b2ddf36b5a9._comment
@@ -4,7 +4,7 @@
  subject="comment 7"
  date="2013-08-26T20:00:39Z"
  content="""
-It's certianly possible that the terminal app eats cpu for some reason even when sitting idle. It's hard for me to tell since I've been measuring cpu use by running top inside that terminal, which necessarily seems to use a lot of the CPU just to draw the screen.
+It's certainly possible that the terminal app eats cpu for some reason even when sitting idle. It's hard for me to tell since I've been measuring cpu use by running top inside that terminal, which necessarily seems to use a lot of the CPU just to draw the screen.
 
 If it's the terminal at fault, it would continue after you shutdown the git-annex daemon, since that doesn't close the terminal.
 """]]
diff --git a/doc/bugs/assistant_doesn__39__t_sync_empty_directories/comment_5_440f349781d7d9ca2d1ed81386f7dd26._comment b/doc/bugs/assistant_doesn__39__t_sync_empty_directories/comment_5_440f349781d7d9ca2d1ed81386f7dd26._comment
new file mode 100644
index 000000000..0d5f0aa29
--- /dev/null
+++ b/doc/bugs/assistant_doesn__39__t_sync_empty_directories/comment_5_440f349781d7d9ca2d1ed81386f7dd26._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 5"
+ date="2013-11-01T22:12:04Z"
+ content="""
+I agree that this is very confusing.  Also having to manually delete empty, renamed directories is...less than ideal.  :)
+"""]]
diff --git a/doc/bugs/assistant_doesn__39__t_sync_file_permissions/comment_3_4d5ae51b4c7e6177d934d7c9f21b912c._comment b/doc/bugs/assistant_doesn__39__t_sync_file_permissions/comment_3_4d5ae51b4c7e6177d934d7c9f21b912c._comment
new file mode 100644
index 000000000..6bf189414
--- /dev/null
+++ b/doc/bugs/assistant_doesn__39__t_sync_file_permissions/comment_3_4d5ae51b4c7e6177d934d7c9f21b912c._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 3"
+ date="2013-11-02T23:49:49Z"
+ content="""
+Dropbox handles permissions, e.g. if I \"chmod -x\" a file on one system, it does the same to my other systems.  It would be a bit of a step backward if git-annex can't do this.  :/  Just my two cents.
+"""]]
diff --git a/doc/bugs/assistant_ignore_.gitignore/comment_2_22f75af80c779dcb4d6033b90373f74e._comment b/doc/bugs/assistant_ignore_.gitignore/comment_2_22f75af80c779dcb4d6033b90373f74e._comment
new file mode 100644
index 000000000..893be9055
--- /dev/null
+++ b/doc/bugs/assistant_ignore_.gitignore/comment_2_22f75af80c779dcb4d6033b90373f74e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnNqLKszWk9EoD4CDCqNXJRIklKFBCN1Ao"
+ nickname="maurizio"
+ subject="git-annex from wheezy-backports should depend on a more recent git version on debian wheezy (7.2) "
+ date="2013-11-12T18:57:52Z"
+ content="""
+It is correct that the bug is solved on the git-annex package found on wheezy-backports, but this package does not force an update of git to a more recent version. Therefore the bug still affects wheezy users. The way to solve it is to install git also from wheezy-backports. 
+
+ 
+"""]]
diff --git a/doc/bugs/assistant_ignore_.gitignore/comment_3_8b2a400e1d44a1c9b183e2b7861efbe3._comment b/doc/bugs/assistant_ignore_.gitignore/comment_3_8b2a400e1d44a1c9b183e2b7861efbe3._comment
new file mode 100644
index 000000000..e58d46084
--- /dev/null
+++ b/doc/bugs/assistant_ignore_.gitignore/comment_3_8b2a400e1d44a1c9b183e2b7861efbe3._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 3"
+ date="2013-11-12T19:10:48Z"
+ content="""
+Agreed, I've made the changes so the next update of the backport will do so.
+"""]]
diff --git a/doc/bugs/data_loss:_incorrect_merge_upon_conflicting_directory-file_of_direct_repos/comment_6_d80c4b631bdf58901a06f29a2c5682e2._comment b/doc/bugs/data_loss:_incorrect_merge_upon_conflicting_directory-file_of_direct_repos/comment_6_d80c4b631bdf58901a06f29a2c5682e2._comment
new file mode 100644
index 000000000..29457da8a
--- /dev/null
+++ b/doc/bugs/data_loss:_incorrect_merge_upon_conflicting_directory-file_of_direct_repos/comment_6_d80c4b631bdf58901a06f29a2c5682e2._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlWskoNgUB7r70OXglR-4iKI4bOuPJb-xg"
+ nickname="Tim"
+ subject="comment 6"
+ date="2013-11-14T14:58:10Z"
+ content="""
+Ah indeed, tried it again and it's indeed fixed. Tried some other things as well, and conflict resolution ended up doing just fine.
+"""]]
diff --git a/doc/bugs/direct_mode_sync_should_avoid_git_commit.mdwn b/doc/bugs/direct_mode_sync_should_avoid_git_commit.mdwn
new file mode 100644
index 000000000..ed4bb8f47
--- /dev/null
+++ b/doc/bugs/direct_mode_sync_should_avoid_git_commit.mdwn
@@ -0,0 +1,5 @@
+Per forum post linking to this bug, git commit can be very slow when run in a filesystem without symlink support, and seems to be reading the content of files just in order to show typechanged messages in the status.
+
+So, git annex sync should stop using git commit when in direct mode, and instead manually make its own commit. Git.Branch.commit and Git.Branch.update should be able to easily be used for this.
+
+PS: this page was created elsewhere, and therefore not listed in bugs page
diff --git a/doc/bugs/get_from_bup-remote_with_pubkey_failing.mdwn b/doc/bugs/get_from_bup-remote_with_pubkey_failing.mdwn
new file mode 100644
index 000000000..5ec1aa9aa
--- /dev/null
+++ b/doc/bugs/get_from_bup-remote_with_pubkey_failing.mdwn
@@ -0,0 +1,93 @@
+### Please describe the problem.
+
+I'm unable to 'git annex get' a file from a bup-remote with encryption set to 'pubkey'.
+
+### What steps will reproduce the problem?
+     
+I added a bup-remote using [these instructions](http://git-annex.branchable.com/walkthrough/using_bup/):
+
+        bash-3.2$ git annex initremote mybup type=bup encryption=pubkey keyid=0xABE8244505D63E81 buprepo=gumdrop:/home/gert/.bup
+
+        # now adding files and moving them:
+        bash-3.2$ mkdir orgmode && touch orgmode/some.org
+        bash-3.2$ git annex add orgmode/some.org
+        add orgmode/some.org (checksum...) ok
+        (Recording state in git...)
+        bash-3.2$ git commit
+        [master bce8c83] Some.org
+         1 file changed, 1 insertion(+)
+         create mode 120000 orgmode/some.org
+        bash-3.2$ git annex move orgmode/ --to=mybup
+        move orgmode/another.org (gpg)
+        U moet een geheime zin opgeven om de geheime sleutel te gebruiken
+        van: “email”
+        4096-bit RSA key, ID 0xFF8DE378DE223820, created 2013-11-10
+                 (sub-sleutel bij hoofd sleutel ID 0xE9B90528FDA4E1E6)
+
+        (checking mybup...) ok
+        (Recording state in git...)
+        bash-3.2$ less orgmode/another.org
+        orgmode/another.org: No such file or directory
+        bash-3.2$ git annex get orgmode/another.org --debug
+        [2013-11-13 16:18:07 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","ls-files","--cached","-z","--","orgmode/another.org"]
+        get orgmode/another.org [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","show-ref","git-annex"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","show-ref","--hash","refs/heads/git-annex"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..f25f9bb2b78a8b9c4b64087f1378c68fb5c0a2f1","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..1b0a3dd72be437d800e58d659837d6e528cbbc39","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..f62419efea58245d232a52ceaf0eaefe3b0fdced","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..eb6f0cd983d9a3637e984aa815537fe20a5c2a69","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..5362118e643462a0875bfe31d493ffe64413f2d8","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] read: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","log","refs/heads/git-annex..e5afaf82ce25f60a108c0ae873b6fd57c5d28ca7","--oneline","-n1"]
+        [2013-11-13 16:18:08 CET] chat: git ["--git-dir=/Users/gert/annex/.git","--work-tree=/Users/gert/annex","cat-file","--batch"]
+        [2013-11-13 16:18:08 CET] read: git ["config","--null","--list"]
+        (from mybup...) (gpg) [2013-11-13 16:18:08 CET] chat: gpg ["--quiet","--trust-model","always","--decrypt"]
+
+        U moet een geheime zin opgeven om de geheime sleutel te gebruiken
+        van: “<email>”
+        4096-bit RSA key, ID 0xFF8DE378DE223820, created 2013-11-10
+                 (sub-sleutel bij hoofd sleutel ID 0xE9B90528FDA4E1E6)
+
+        [2013-11-13 16:18:15 CET] read: bup ["join","-r","gumdrop:/home/gert/.bup","GPGHMACSHA1--67aec1b62d05d000442cf8e7d9df8d327eaf26d5"]
+        [2013-11-13 16:18:15 CET] chat: gpg ["--quiet","--trust-model","always","--batch","--decrypt"]
+        gpg: kan geheime zin niet opvragen in batch modus
+        gpg: decoderen mislukt: secret key not available
+
+          Unable to access these remotes: mybup
+
+          Try making some of these repositories available:
+          080e97d2-4f82-4292-acb7-a48d82009258 -- mybup (mybupmy bup repository at gumdrop)
+
+          (Note that these git remotes have annex-ignore set: origin)
+        failed
+        git-annex: get: 1 failed
+
+### What version of git-annex are you using? On what operating system?
+
+Running git-annex version 4.20131105-g136b030 on OSX 10.8.5.
+
+### Please provide any additional information below.
+
+My ideas:
+
+"Unable to access these remotes: mybup" is weird, I just moved files there.
+
+"secret key not available" makes me think it's looking for the primary secret key (which is indeed offline).
+When I encrypt a file with the same key I used to create the remote it just works:
+
+    $ gpg --armor --recipient 0xABE8244505D63E81 --encrypt file.txt
+    $ gpg --decrypt file.txt.asc
+
+When prompting for my passphrase it states "4096-bit RSA key, ID 0xFF8DE378DE223820, created 2013-11-10".
+That is a different subkey than what I entered when I setting up the remote.
+
+My keys/subkeys:
+
+    pub  4096R/0xE9B90528FDA4E1E6  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: SC
+                               vertrouwen: ultimate      geldigheid: ultimate
+    sub  4096R/0x98816CFB398B4666  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: E
+    sub  4096R/0x91951718D5F11CDD  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: S
+    sub  4096R/0xABE8244505D63E81  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: E
+    sub  4096R/0xB44520A46B27144D  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: S
+    sub  4096R/0xFF8DE378DE223820  aangemaakt: 2013-11-10  vervaldatum: 2014-11-10  gebruik: E
+
+> This was already fixed in version 4.20131106. [[done]] --[[Joey]] 
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied.mdwn b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied.mdwn
new file mode 100644
index 000000000..260ab9981
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied.mdwn
@@ -0,0 +1,48 @@
+### Please describe the problem.
+I followed the tip on [fully encrypted git repositories with gcrypt](http://git-annex.branchable.com/tips/fully_encrypted_git_repositories_with_gcrypt/) to create encrypted git-annex repository on a ssh server. When I try to checkout the repository, things break as follows:
+
+`git clone gcrypt::ssh://my.server/home/me/encryptedrepo myrepo` 
+
+works as expected but when in the myrepo directory, 
+
+`git annex enableremote encryptedrepo gitrepo=ssh://my.server/home/me/encryptedrepo`
+
+issues the following text (among normal messages):
+
+`git-annex-shell: gcryptsetup permission denied`
+
+Then while the links are there, 
+
+`git annex get --from encryptedrepo`
+
+does nothing (in the sense that the content is not retrieved). 
+
+This seems to have everything to do with git-annex-shell as the exact same manipulations but with a local repository work perfectly. Unfortunately, I don't know haskell so [this code](https://github.com/joeyh/git-annex/blob/master/Command/GCryptSetup.hs) is cryptic to me. I can guess there is a problem getting the uuid of the repository, but as far as I can tell the bare distant repo looks fine. 
+
+### What steps will reproduce the problem?
+
+Create a standard git annex local repository and then follow the [fully encrypted git repositories with gcrypt tip](http://git-annex.branchable.com/tips/fully_encrypted_git_repositories_with_gcrypt/) to create an encrypted git-annex repository on a ssh server. Then follow the instructions in the same tip to clone the remote repository. 
+
+### What version of git-annex are you using? On what operating system?
+Both computers run ubuntu 12.04 with all updates and the latest git annex from the ppa, that is:
+
+git-annex version: 4.20131024
+
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP Feeds Quvi TDFA
+
+key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
+
+remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_1_f4584158b35b80ece1060308883e2dc4._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_1_f4584158b35b80ece1060308883e2dc4._comment
new file mode 100644
index 000000000..6312a58a5
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_1_f4584158b35b80ece1060308883e2dc4._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-02T19:46:28Z"
+ content="""
+It seems to me that the `git-annex-shell` on the remote system must be too old a version to support the gcryptsetup command. You can check this by running `git-annex-shell` there and seeing if it lists gcryptsetup in its usage message.
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_2_a4d7aae848340771a9b8e2c87abeea42._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_2_a4d7aae848340771a9b8e2c87abeea42._comment
new file mode 100644
index 000000000..f2fb4f14f
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_2_a4d7aae848340771a9b8e2c87abeea42._comment
@@ -0,0 +1,26 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="comment 2"
+ date="2013-11-02T21:53:37Z"
+ content="""
+The git-annex version on the remote server is the same as the one on the client, the latest one available from the ppa (4.20131024). When I run git-annex-shell on both computers, I obtain:
+[[!format sh \"\"\"
+git-annex-shell: bad parameters
+
+Usage: git-annex-shell [-c] command [parameters ...] [option ...]
+
+Plumbing commands:
+
+commit       DIRECTORY          commits any staged changes to the git-annex branch
+configlist   DIRECTORY          outputs relevant git configuration
+dropkey      DIRECTORY KEY ...  drops annexed content for specified keys
+gcryptsetup  DIRECTORY VALUE    sets up gcrypt repository
+inannex      DIRECTORY KEY ...  checks if keys are present in the annex
+recvkey      DIRECTORY KEY      runs rsync in server mode to receive content
+sendkey      DIRECTORY KEY      runs rsync in server mode to send content
+transferinfo DIRECTORY KEY      updates sender on number of bytes of content received
+\"\"\"]]
+
+Both sides seem to understand the gcryptsetup action. Actually, the message gcryptsetup permission denied comes from git-annex-shell, as far as I understand (and from the haskell source linked in the report). 
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_3_06bda101ad584b4b882de8b2e202d679._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_3_06bda101ad584b4b882de8b2e202d679._comment
new file mode 100644
index 000000000..863f401ce
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_3_06bda101ad584b4b882de8b2e202d679._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T23:51:13Z"
+ content="""
+I should have looked at that error message more closely. The gcryptsetup command will print a permission denied if the repository it's being run in already has a annex.uuid or already has a gcrypt id. Probably that latter needs to be relaxed for enableremote to work.
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_4_4fc6b25401b645cabc04b510bdfa6863._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_4_4fc6b25401b645cabc04b510bdfa6863._comment
new file mode 100644
index 000000000..e1049ce60
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_4_4fc6b25401b645cabc04b510bdfa6863._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 4"
+ date="2013-11-03T00:15:30Z"
+ content="""
+While I've fixed this bug, in my testing the bug only caused git-annex to fall back to accessing the remote repository using rsync, rather than using git-annex-shell to talk to it, and so `git annex get --from encryptedrepo` was able to retrieve files that were stored in that remote despite the bug. That may have failed for you for some other reason.
+
+You can set git.encryptedrepo.annex-gcrypt to to \"true\" to make it use the degraded rsync mode, or to \"shell\" to make it use git-annex-shell. Setting it to shell should be all that you need to do to recover from (or indeed, work around this bug).
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_5_4e193306801680bba433e75eb4dcba05._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_5_4e193306801680bba433e75eb4dcba05._comment
new file mode 100644
index 000000000..137638aa5
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_5_4e193306801680bba433e75eb4dcba05._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="comment 5"
+ date="2013-11-03T11:24:28Z"
+ content="""
+There is something very strange that I did not notice in my first report. When I try `git annex get --from encryptedrepo` nothing happens in the sense that git annex is not even trying to connect to the remote (no ssh connection attempt) while git.encryptedrepo.annex-gcrypt is set to true. When I set it to shell, nothing happens either. 
+
+Another thing I did not report is that I tried the exact same manipulations with another server on which git annex is not installed. The `gcryptsetup permission denied` message was replaced by a `git-annex-shell not found` (or something similar), as expected. But the rest of the behavior was the same: no way to get the actual content with `git annex get --from`. Again, all of this is with 4.20131024, not with the ongoing version. 
+
+I'll try got do more test with the new version. 
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_6_76ccdf0542e76e4dbd61f3b3228d40ba._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_6_76ccdf0542e76e4dbd61f3b3228d40ba._comment
new file mode 100644
index 000000000..0ad9768f6
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_6_76ccdf0542e76e4dbd61f3b3228d40ba._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 6"
+ date="2013-11-04T17:12:05Z"
+ content="""
+It's entirely normal for `git annex get --from remote` to skip files that it does not think are present on the remote. 
+
+What does `git annex whereis` say?
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_7_cd964d0a375c5cba299bf2bbbbb86acb._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_7_cd964d0a375c5cba299bf2bbbbb86acb._comment
new file mode 100644
index 000000000..3a24f4349
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_7_cd964d0a375c5cba299bf2bbbbb86acb._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="comment 7"
+ date="2013-11-04T18:54:54Z"
+ content="""
+`git annex whereis` says the files are not on the remote git, while they are because of the copy. If I do _exactly_ what's on the tip, that is if I clone the encrypted git just after having done `git annex copy --to encryptedbackup`, the remotes seems to ignore that it has the data. To have it working, I had to call `git annex sync` (push will do, I guess) in the original remote after doing the `git annex copy`. Then I can `git pull` and `git annex whereis` knows where the files are (or I can clone the encrypted remote after doing the sync/pull). 
+
+It seems a bit strange that the copy command does not record the propagation of the file to the encrypted git. I guess this is because gcrypt is the only special remote that stores also the git part, right? Would that be a good idea (and possible) to handle it in a special way? 
+
+Thanks Joey for everything, by the way, both the software and the amazing support via email and the website.
+"""]]
diff --git a/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_8_9bac87c85deb5bb15795df28533d0cde._comment b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_8_9bac87c85deb5bb15795df28533d0cde._comment
new file mode 100644
index 000000000..da2fef585
--- /dev/null
+++ b/doc/bugs/git-annex-shell:_gcryptsetup_permission_denied/comment_8_9bac87c85deb5bb15795df28533d0cde._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 8"
+ date="2013-11-04T19:14:04Z"
+ content="""
+Right -- Normally a special remote doesn't include a git repository. And when using a regular git remote, `git-annex-shell` is used to receive files into the repository and it records immediately that the repo has the file so there's no need to sync in that case. So gcrypt is special in this way.
+
+For now, I have fixed the tip to show syncing after sending files to gcrypt. It might be the case that it would make sense to do a push of the git-annex branch automatically in that case, will have to think about that and see if people get tripped up on this.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3.mdwn b/doc/bugs/git-annex_broken_on_Android_4.3.mdwn
index da1f7fd28..4c1b356fb 100644
--- a/doc/bugs/git-annex_broken_on_Android_4.3.mdwn
+++ b/doc/bugs/git-annex_broken_on_Android_4.3.mdwn
@@ -1,3 +1,7 @@
 As per [[install/Android/#comment-e218073735d67691a2c3f66cc53ca6ac]] and [[install/Android/#comment-29bd13ab9cb830ffcd7850b84fb111c8]] :
 
 git-annex is broken on Android 4.3; both on Nexus 4 and Nexus 7.
+
+> [[Fixed|done]]. A 4.3 build of the apk is now available.  
+> (Unfortunately the fix breaks support for older versions of Android, 
+> so two versions of the apk have to be built now.) --[[Joey]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_10_e47c073f1614f7b57f86acedeeb1cadc._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_10_e47c073f1614f7b57f86acedeeb1cadc._comment
new file mode 100644
index 000000000..5d56dc84c
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_10_e47c073f1614f7b57f86acedeeb1cadc._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawm7qEQF8yzbY0_PHq3QERHxUGuXmW6qw8o"
+ nickname="Anton"
+ subject="comment 10"
+ date="2013-11-10T22:10:49Z"
+ content="""
+I can confirm that the Hello World program works with the Nexus 7 2013, running Android 4.3.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_11_ce34578c45060b7c8b759efd1c1d8df8._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_11_ce34578c45060b7c8b759efd1c1d8df8._comment
new file mode 100644
index 000000000..d84a59b76
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_11_ce34578c45060b7c8b759efd1c1d8df8._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Hooray!"
+ date="2013-11-10T22:21:46Z"
+ content="""
+I have a Nexus 7 (2013) with 4.3 that I'll test it on---I expect that my test will be successful.
+
+I'll also run the test on my Nexus 5, running 4.4.
+
+Getting git-annex working on 4.3 was the last thing keeping me from being able to ditch Dropbox entirely.  I'm so glad to hear there's some potential progress.
+
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_12_75965395dc33046ce34ac5ba972b7d64._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_12_75965395dc33046ce34ac5ba972b7d64._comment
new file mode 100644
index 000000000..3f520d7e4
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_12_75965395dc33046ce34ac5ba972b7d64._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 12"
+ date="2013-11-10T22:23:49Z"
+ content="""
+Full rebuild in progress (takes about 6 hours +- manual fixing).
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_13_f07bc76dd3c5580fc0855a33ae835c8d._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_13_f07bc76dd3c5580fc0855a33ae835c8d._comment
new file mode 100644
index 000000000..f2a57f731
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_13_f07bc76dd3c5580fc0855a33ae835c8d._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Oh, and if a 4.3 device would be helpful..."
+ date="2013-11-10T22:28:48Z"
+ content="""
+I have Samsung Epic 4G (epic_mtd) that I'm no longer using and would be quite happy to send you---it's older, and slow, but it is at least currently supported by CyanogenMod, so it should be possible to install 10.2 milestone builds on it and at least do basic testing.
+
+Hell, if it would really facilitate Android support, I'd happily pick up something like a B&N Nook HD+ and send it to you---that should be similarly amenable to CM installs and testing.
+
+Though I will also understand if you don't necessarily want to have a bunch of superfluous hardware laying around.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_14_637c59becc68a1e4f60069d8873489ff._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_14_637c59becc68a1e4f60069d8873489ff._comment
new file mode 100644
index 000000000..6336a3bd4
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_14_637c59becc68a1e4f60069d8873489ff._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Works on KitKat"
+ date="2013-11-10T23:15:28Z"
+ content="""
+I skipped testing on my Nexus 7, figuring that would be duplicative, and instead ran it on my Nexus 5, and it worked great.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_15_d80b87055f72873f5678a01d2630bea4._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_15_d80b87055f72873f5678a01d2630bea4._comment
new file mode 100644
index 000000000..6bca41b3a
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_15_d80b87055f72873f5678a01d2630bea4._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 15"
+ date="2013-11-11T04:34:21Z"
+ content="""
+6 hours later, and: <http://downloads.kitenet.net/git-annex/autobuild/android/git-annex.apk>
+
+testing appreciated!
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_16_57ac84868b223b30f005704eefa01b8d._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_16_57ac84868b223b30f005704eefa01b8d._comment
new file mode 100644
index 000000000..204845eb5
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_16_57ac84868b223b30f005704eefa01b8d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://launchpad.net/~subito"
+ nickname="subito"
+ subject="Nexus 5 Android 4.4"
+ date="2013-11-11T10:07:07Z"
+ content="""
+Does not work for me. Same error as in the original Bug report.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_17_a41f4d8a72c07ad770e6479e9b8c7f1d._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_17_a41f4d8a72c07ad770e6479e9b8c7f1d._comment
new file mode 100644
index 000000000..9712f5944
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_17_a41f4d8a72c07ad770e6479e9b8c7f1d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Same error as before, Nexus 5 and 7"
+ date="2013-11-11T13:06:17Z"
+ content="""
+Unfortunately, my experience mirrors subito's---same error as before on both 4.3 and 4.4.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_18_7d36637f11cda51de395303d5c1c6a3f._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_18_7d36637f11cda51de395303d5c1c6a3f._comment
new file mode 100644
index 000000000..2dc32cf15
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_18_7d36637f11cda51de395303d5c1c6a3f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 18"
+ date="2013-11-11T13:27:49Z"
+ content="""
+Hmm, maybe the problem is caused by stripping the program? If so, this should fail the same way: <http://tmp.kitenet.net/hello.stripped>
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_19_c8609c3f7f62ae5427fd8c60bc9546ed._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_19_c8609c3f7f62ae5427fd8c60bc9546ed._comment
new file mode 100644
index 000000000..2f22ad21c
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_19_c8609c3f7f62ae5427fd8c60bc9546ed._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Unfortunately, it would not appear that easy..."
+ date="2013-11-11T14:33:05Z"
+ content="""
+The stripped binary for hello worked fine.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_20_0886bca6d0c6a9415a7794d256be2e9d._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_20_0886bca6d0c6a9415a7794d256be2e9d._comment
new file mode 100644
index 000000000..2b547d9a7
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_20_0886bca6d0c6a9415a7794d256be2e9d._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 20"
+ date="2013-11-11T16:23:11Z"
+ content="""
+To bisect the problem space further, in case the apk build machinery is at fault, here's a git-annex binary not included in an apk. (Run same as the hello world.)
+
+<http://tmp.kitenet.net/git-annex.bin>
+
+And here's a more minimal git-annex binary (trying to look identical to hello world from the linker's perspective, just a bit larger..).
+
+<http://tmp.kitenet.net/git-annex-min.bin>
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_21_2b39729f95c9c4bba620ecdd3d1558ed._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_21_2b39729f95c9c4bba620ecdd3d1558ed._comment
new file mode 100644
index 000000000..551334819
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_21_2b39729f95c9c4bba620ecdd3d1558ed._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmqz6wCn-Q1vzrsHGvEJHOt_T5ZESilxhc"
+ nickname="Sören"
+ subject="Galaxy S4 Android 4.3"
+ date="2013-11-11T18:47:23Z"
+ content="""
+hello and hello.stripped both work here but the git-annex binaries don't (still the same error as in the bug report). 
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_22_8d90d92951919aa70638b31e9248bec5._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_22_8d90d92951919aa70638b31e9248bec5._comment
new file mode 100644
index 000000000..e4937e0f8
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_22_8d90d92951919aa70638b31e9248bec5._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Both fail..."
+ date="2013-11-11T18:53:34Z"
+ content="""
+Same linking issue for both.
+
+I don't *think* it should make any difference at all, but to spare myself a little bit of typing on this soft keyboard, I'm using a small variation on your script; I'm sharing it so other testers can use it, too, and so someone can point out if I'm doing something wrong:
+
+    D=/data/data/ga/androidterm/tmp/gatest
+    cp <file> $D
+    chmod +x $D
+    $D
+
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_23_6398271f5cd9e94996202ef3bce6f6ed._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_23_6398271f5cd9e94996202ef3bce6f6ed._comment
new file mode 100644
index 000000000..05cb634e6
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_23_6398271f5cd9e94996202ef3bce6f6ed._comment
@@ -0,0 +1,20 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 23"
+ date="2013-11-11T19:14:59Z"
+ content="""
+Script variation is ok.
+
+So, it's looking like perhaps a problem with the way cabal links the executable, which I notice is a two stage process, vs the way ghc links it with --make.
+
+To narrow down, here is hello built using cabal:
+
+<http://tmp.kitenet.net/hello-cabal>
+
+Here is git-annex built not using cabal:
+
+<http://tmp.kitenet.net/git-annex-byhand>
+
+(For my own reference, it's also built without WITH_CLIBS.)
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_24_c9e399833cc6235077161f490dfa866f._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_24_c9e399833cc6235077161f490dfa866f._comment
new file mode 100644
index 000000000..c8fea212b
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_24_c9e399833cc6235077161f490dfa866f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmqz6wCn-Q1vzrsHGvEJHOt_T5ZESilxhc"
+ nickname="Sören"
+ subject="comment 24"
+ date="2013-11-11T19:56:04Z"
+ content="""
+hello-cabal working, git-annex-byhand not.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_25_cf093737eefb2b99f6f0eac9bf3e74b3._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_25_cf093737eefb2b99f6f0eac9bf3e74b3._comment
new file mode 100644
index 000000000..e28a9508b
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_25_cf093737eefb2b99f6f0eac9bf3e74b3._comment
@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="I got the same results as Sören."
+ date="2013-11-11T20:37:08Z"
+ content="""
+cabal doesn't seem to be the culprit.
+
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_26_c122ce53175fc9e0e114a8acd2385c0d._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_26_c122ce53175fc9e0e114a8acd2385c0d._comment
new file mode 100644
index 000000000..1c72cd27b
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_26_c122ce53175fc9e0e114a8acd2385c0d._comment
@@ -0,0 +1,29 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="finally getting debugger spun up"
+ date="2013-11-12T01:08:24Z"
+ content="""
+<https://code.google.com/p/android/issues/detail?id=28598> seems relevant (and the patches to fix it seem likely to have led to the linker rejecting this).
+
+So I can probably stop torturing your soft keyboards. I need a binary where `arm-linux-androideabi-4.8/bin/arm-linux-androideabi-readelf -r` does not contain `R_ARM_COPY`. Checking against the binaries so far, this consistently matches the test results, all the git-annex binaries have:
+
+<pre>
+ Offset     Info    Type            Sym.Value  Sym. Name
+011d05f0  00004e14 R_ARM_COPY        011d05f0   environ
+</pre>
+
+(Which is itself interesting; I've had to work around some problems with the haskell port not supporting getting the environment (Annex.Branch.withIndex). Possibly because it was copied and the linker screwed that up? <https://github.com/neurocyte/ghc-android/issues/7>)
+
+Ok, here's a binary that meets those criteria. Obtained by passing -z nocopyreloc to the gold linker (ghc options -optl-z -optlnocopyreloc)
+
+<http://tmp.kitenet.net/git-annex-nocopy>
+
+Also, here's a hello world binary that *should* fail. It attempts to read and print the environment, and has the same `R_ARM_COPY` relocation.
+
+<http://tmp.kitenet.net/hello-env-copy>
+
+And, here's a hello world binary that *might* successfully print out the full environment (like `set` does). If it does, I can also remove the ugly hack in Annex.Branch.withIndex. Which would be an unexpected reward.
+
+<http://tmp.kitenet.net/hello-env-nocopy>
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_27_237e41e61781bb058f5fd39362a904e4._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_27_237e41e61781bb058f5fd39362a904e4._comment
new file mode 100644
index 000000000..dd911955a
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_27_237e41e61781bb058f5fd39362a904e4._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="nocopy variants work!"
+ date="2013-11-12T03:17:09Z"
+ content="""
+I tested both the hello-env-nocopy and the git-annex-nocopy binaries successfully.  hello-env-copy failed as you predicted.
+
+Yay!
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_28_97f423a41ee9d2d74291594fae20dd4e._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_28_97f423a41ee9d2d74291594fae20dd4e._comment
new file mode 100644
index 000000000..6341aae80
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_28_97f423a41ee9d2d74291594fae20dd4e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 28"
+ date="2013-11-12T03:58:56Z"
+ content="""
+This fix is now in place in the android autobuilds.
+
+Just to be sure, hello-env-nocopy managed to print out multiple environment variables?
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_29_7b3fbe7e38f637fcea511441ac243d93._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_29_7b3fbe7e38f637fcea511441ac243d93._comment
new file mode 100644
index 000000000..1cd4c356f
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_29_7b3fbe7e38f637fcea511441ac243d93._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmqz6wCn-Q1vzrsHGvEJHOt_T5ZESilxhc"
+ nickname="Sören"
+ subject="APK now works too"
+ date="2013-11-12T09:10:49Z"
+ content="""
+I got the same results as Michael. The output of hello-nocopy is a longer list of environment variables.
+Even better, the apk from the autobuilder now seems to work fine as well, including the webapp.
+Great work! Thanks for digging into this.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_30_26c04584c3c6dacf59e1b6c82042c97c._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_30_26c04584c3c6dacf59e1b6c82042c97c._comment
new file mode 100644
index 000000000..3409b9c4a
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_30_26c04584c3c6dacf59e1b6c82042c97c._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnegApaT6kTI0Gxy9SNmI9Og-k_fC_aS7Y"
+ nickname="Michael Alan"
+ subject="Yep, the env was printed"
+ date="2013-11-12T10:18:56Z"
+ content="""
+I would recognize the output of a Show instance anywhere.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_8_f58897eff6b4693f0c73474ccfe6e733._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_8_f58897eff6b4693f0c73474ccfe6e733._comment
new file mode 100644
index 000000000..52326b8e2
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_8_f58897eff6b4693f0c73474ccfe6e733._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmhfodZquCI_EEl-f3h7HkROTszlsQL6yA"
+ nickname="Joe"
+ subject="Samsung Galaxy S4 also affected"
+ date="2013-11-09T02:47:54Z"
+ content="""
+Verizon just pushed out 4.3 to Samsung Galaxy S4 devices. This issue is affecting me now too.
+"""]]
diff --git a/doc/bugs/git-annex_broken_on_Android_4.3/comment_9_ddba87b2f20d8a63f7b8ebdb9bd13515._comment b/doc/bugs/git-annex_broken_on_Android_4.3/comment_9_ddba87b2f20d8a63f7b8ebdb9bd13515._comment
new file mode 100644
index 000000000..015efd7ce
--- /dev/null
+++ b/doc/bugs/git-annex_broken_on_Android_4.3/comment_9_ddba87b2f20d8a63f7b8ebdb9bd13515._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 9"
+ date="2013-11-10T20:12:47Z"
+ content="""
+I have finally managed to get ghc to build with the newest version of the NDK. I hope this means it will make binaries that work with 4.3, but I don't have a device to test.
+
+Here is a hello world program built with it:
+<http://tmp.kitenet.net/hello>
+
+After downloading it to an Android device, you can test it by opening the
+git-annex terminal, and running: `D=/data/data/ga.androidterm/tmp; cp hello $D; chmod +x $D/hello; $D/hello`
+
+Tested working on android 4.0.4
+
+Also, I have filed a bug upstream about this at <https://github.com/neurocyte/ghc-android/issues/23>
+"""]]
diff --git a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_7_0f4f471102e394ebb01da40e4d0fd9f6._comment b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_7_0f4f471102e394ebb01da40e4d0fd9f6._comment
index c3aee6c57..92b205bc3 100644
--- a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_7_0f4f471102e394ebb01da40e4d0fd9f6._comment
+++ b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_7_0f4f471102e394ebb01da40e4d0fd9f6._comment
@@ -6,7 +6,7 @@
  content="""
 git 1.7.4 does not make things better. With it, if I add first \"X/foo\" and then \"x/bar\", it commits \"X/bar\".
 
-That will *certianly* cause problems when interoperating with a repo clone on a case-sensative filesystem, since
+That will *certainly* cause problems when interoperating with a repo clone on a case-sensative filesystem, since
 git-annex there will not see the location log that git committed to the wrong case directory.
 
 It's possible there is some interoperability problem when pulling from linux like you did, onto HFS+, too. I am not quite sure. Ah, I did find one.. if I clone the repo with \"X/foo\" in it to a case-sensative filesystem, and add a \"x/foo\" there,
diff --git a/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights.mdwn b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights.mdwn
new file mode 100644
index 000000000..b36d5e84c
--- /dev/null
+++ b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights.mdwn
@@ -0,0 +1,19 @@
+### Please describe the problem.
+
+Installing on Windows requires installing git followed by git-annex. Installing the former works without admin rights, but the latter cannot be installed afterwards.
+
+### What steps will reproduce the problem?
+
+1. Create a Windows account without admin rights
+2. Install git
+3. Install git-annex
+
+### What version of git-annex are you using? On what operating system?
+
+Latest release on MS Windows.
+
+### Please provide any additional information below.
+
+
+Installing git creates read-only directories that cannot be used by the git-annex install afterwards. Without admin rights, the read-only flag of the git dir cannot be altered.
+
diff --git a/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_1_2533800ab5a95c5d71c3b47a630e751a._comment b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_1_2533800ab5a95c5d71c3b47a630e751a._comment
new file mode 100644
index 000000000..32fc0311e
--- /dev/null
+++ b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_1_2533800ab5a95c5d71c3b47a630e751a._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T16:19:41Z"
+ content="""
+Thanks, this had been reported in the forum before, but they did not point at the directory permissions as the problem.
+
+It would be possible to modify the installer to install git-annex somewhere else and add it to the PATH, but it seems this is a utter nightmare on windows and I'd have to pull in enormous NSIS scripts from their wiki, of unknown provenance. Which is why I am piggybacking on the git installation's PATH.
+"""]]
diff --git a/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_2_5b71785acf16a8d9ea457726599daef3._comment b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_2_5b71785acf16a8d9ea457726599daef3._comment
new file mode 100644
index 000000000..4bd5c2c0e
--- /dev/null
+++ b/doc/bugs/git-annex_does_not_install_on_windows_without_admin_rights/comment_2_5b71785acf16a8d9ea457726599daef3._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://me.yahoo.com/a/bBy7WkgQicYHIiiyj.Vm0TcMbxi2quzbPFef#6f9f7"
+ nickname="Frederik Vanrenterghem"
+ subject="comment 2"
+ date="2013-11-26T21:57:28Z"
+ content="""
+Just wondering how git succeeds in installing as non-admin user. The folder it goes in is also read-only.
+"""]]
diff --git a/doc/bugs/git-annex_merge_stalls/comment_3_ced9b0d724fb55c756106b64c3721003._comment b/doc/bugs/git-annex_merge_stalls/comment_3_ced9b0d724fb55c756106b64c3721003._comment
index 600044354..382f8c835 100644
--- a/doc/bugs/git-annex_merge_stalls/comment_3_ced9b0d724fb55c756106b64c3721003._comment
+++ b/doc/bugs/git-annex_merge_stalls/comment_3_ced9b0d724fb55c756106b64c3721003._comment
@@ -12,7 +12,7 @@ joeyh for example, if you ran it and ctrl-z'd at just the right time, it could b
 joeyh (or the kernel coud have gotten confused, which given you also had a crash, who knows..)
 dp sounds logical
 joeyh forcing locks is always a problimatic thing
-joeyh but git-annex could certianly notice if it seems to be stalled and print some useful messages
+joeyh but git-annex could certainly notice if it seems to be stalled and print some useful messages
 joeyh and maybe have a way to run with locks forced
 </pre>
 """]]
diff --git a/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_1_8f081aeba7065d143a453dc128543f59._comment b/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_1_8f081aeba7065d143a453dc128543f59._comment
index 99bc8277d..89531ca16 100644
--- a/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_1_8f081aeba7065d143a453dc128543f59._comment
+++ b/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_1_8f081aeba7065d143a453dc128543f59._comment
@@ -14,5 +14,5 @@ The link that you show:
 
 If I understand you correctly, it's only happening with one particular file content.
 
-I think you either need to rule out it being due to the way you've installed git-annex, perhaps by installing the linux standalone tarball, and seeing if you can get the same behavior with that. Or you could send me the repository by email (joey@kitenet.net) and I'll see if I can reproduce it, and if so, will certianly be able to debug and fix it.
+I think you either need to rule out it being due to the way you've installed git-annex, perhaps by installing the linux standalone tarball, and seeing if you can get the same behavior with that. Or you could send me the repository by email (joey@kitenet.net) and I'll see if I can reproduce it, and if so, will certainly be able to debug and fix it.
 """]]
diff --git a/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_2_54a4b10723fd8a80dd486377ff15ce0d._comment b/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_2_54a4b10723fd8a80dd486377ff15ce0d._comment
index 1aefe452d..7ac34e751 100644
--- a/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_2_54a4b10723fd8a80dd486377ff15ce0d._comment
+++ b/doc/bugs/git_annex_add_removes_file_with_no_data_left/comment_2_54a4b10723fd8a80dd486377ff15ce0d._comment
@@ -4,7 +4,7 @@
  subject="comment 2"
  date="2013-07-18T19:46:12Z"
  content="""
-Hmm, given the size of the repo, please don't email it directly, if you choose to do that. But getting me access to it would certianly be useful.
+Hmm, given the size of the repo, please don't email it directly, if you choose to do that. But getting me access to it would certainly be useful.
 
 
 """]]
diff --git a/doc/bugs/git_annex_describe_can_break_uuid.log.mdwn b/doc/bugs/git_annex_describe_can_break_uuid.log.mdwn
new file mode 100644
index 000000000..16e6981f5
--- /dev/null
+++ b/doc/bugs/git_annex_describe_can_break_uuid.log.mdwn
@@ -0,0 +1,46 @@
+### Please describe the problem.
+
+`uuid.log` can end up in a state where `git annex describe` (and probably other things) stops working.
+
+### What steps will reproduce the problem?
+
+Run `git annex describe` against a remote that is not a an initialized git-annex repo.
+
+### What version of git-annex are you using? On what operating system?
+
+debian-packaged git-annex 4.20131106 on Linux Mint 13/Maya (Ubuntu Precise/12.04)
+
+### Please provide any additional information below.
+
+I will follow comments, but can also be found at [[https://microca.st/clacke]].
+
+Full transcript to reproduce:
+
+[[!format sh """
+$ git init a
+Initialized empty Git repository in /tmp/annex/a/.git/
+$ git init b
+Initialized empty Git repository in /tmp/annex/b/.git/
+$ cd a/
+$ git annex init
+init  ok
+(Recording state in git...)
+$ git remote add -f b ../b
+Updating b
+$ git annex describe b b # this should not be ok
+describe b ok
+(Recording state in git...)
+$ git annex describe b b
+describe b git-annex: Prelude.last: empty list
+$ git cat-file blob git-annex:uuid.log
+ b timestamp=1383987654.900868s
+...
+
+# End of transcript.
+"""]]
+
+> Fixed the bug and made git breakage not crash git-annex. [[done]]
+> --[[Joey]] 
+
+> > Update: Also made it automatically clean up the cruft this put in the
+> > log. --[[Joey]] 
diff --git a/doc/bugs/git_annex_describe_can_break_uuid.log/comment_2_9ead36f13cbde6c822b231441de636ae._comment b/doc/bugs/git_annex_describe_can_break_uuid.log/comment_2_9ead36f13cbde6c822b231441de636ae._comment
new file mode 100644
index 000000000..a5616234e
--- /dev/null
+++ b/doc/bugs/git_annex_describe_can_break_uuid.log/comment_2_9ead36f13cbde6c822b231441de636ae._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 2"
+ date="2013-11-11T05:32:14Z"
+ content="""
+Great, thanks!
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9.mdwn b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9.mdwn
index 372c06ba9..2169372a2 100644
--- a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9.mdwn
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9.mdwn
@@ -216,3 +216,5 @@ Binary Images:
 
 # End of transcript or log.
 """]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_19_9881db7bb6fef4e47c54cdc23e995f17._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_19_9881db7bb6fef4e47c54cdc23e995f17._comment
new file mode 100644
index 000000000..96356e047
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_19_9881db7bb6fef4e47c54cdc23e995f17._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnt7phVzBQ0xO5rCO6sfmEmxQItmFMyqls"
+ nickname="Kevin"
+ subject="comment 19"
+ date="2013-11-02T00:58:31Z"
+ content="""
+I tried @flabbergast's dmg.  It seems to work fine (including the web app) on my Air, but the web app fails on my iMac with
+
+    $ git annex webapp
+    Launching web browser on file:///Users/kw/Desktop/annex/.git/annex/webapp.html
+    error: git-annex died of signal 4
+    $
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_20_41e2ea458669f59f96b5860825745910._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_20_41e2ea458669f59f96b5860825745910._comment
new file mode 100644
index 000000000..fca9ba58e
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_20_41e2ea458669f59f96b5860825745910._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnt7phVzBQ0xO5rCO6sfmEmxQItmFMyqls"
+ nickname="Kevin"
+ subject="comment 20"
+ date="2013-11-02T01:02:18Z"
+ content="""
+Also, to avoid hurt feelings etc., it might be best to make it clear on your home page and kickstarter that you do not intend to support OS X yourself.
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_21_515039e321e0595f95430d8082bd54a5._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_21_515039e321e0595f95430d8082bd54a5._comment
new file mode 100644
index 000000000..a0a175d30
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_21_515039e321e0595f95430d8082bd54a5._comment
@@ -0,0 +1,20 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 21"
+ date="2013-11-08T19:22:17Z"
+ content="""
+Now that I can try running the 10.8 dmg on 10.9 myself, I get this failure:
+
+<pre>
+oberon:~ joeyh$ /Volumes/git-annex/git-annex.app/Contents/MacOS/git-annex
+dyld: Symbol not found: _objc_debug_taggedpointer_mask
+  Referenced from: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
+  Expected in: /Volumes/git-annex/git-annex.app/Contents/MacOS/bundle/I
+ in /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
+</pre>
+
+This makes me think that that adding back the OSX frameworks might possibly yield a dmg that can work on both versions. Although that's probably more likely to work if it's built on 10.8 and used on 10.9 than the other way around. Might be worth a try to revert commit 900351ab8585c171486cef853eff4a95ec151e6f and commit 9b663c7f8cf82cee523b75be1a8786fa7d34b428 to try that.
+
+Oh well, I should have a native 10.9 dmg autobuild set up before too long. 10.8 autobuilder has built its last image unfortunately, due to being upgraded to 10.9.
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_22_9412236296871c570c66f5b4c7f9681e._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_22_9412236296871c570c66f5b4c7f9681e._comment
new file mode 100644
index 000000000..e5942bfd4
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_22_9412236296871c570c66f5b4c7f9681e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 22"
+ date="2013-11-14T18:55:54Z"
+ content="""
+Native 10.9 autobuilder is now running. <https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mavericks/git-annex.dmg.bz2>
+
+Lacks XMPP support until I get libxml2 linked on the autobuilder. Only tested on the build machine so far.
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_23_e4e7d13be6c0bc63f426e535de6172f8._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_23_e4e7d13be6c0bc63f426e535de6172f8._comment
new file mode 100644
index 000000000..db8d835d2
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_23_e4e7d13be6c0bc63f426e535de6172f8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnmF_9CAtfqdZkC4e-_dCX-rK5bqh4RWkw"
+ nickname="Carl"
+ subject="comment 23"
+ date="2013-11-14T19:22:16Z"
+ content="""
+Seems to work on my Mavericks Macbook Air. Thank you!
+"""]]
diff --git a/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_24_c73e1277c5f284b1019362fb2bef94a8._comment b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_24_c73e1277c5f284b1019362fb2bef94a8._comment
new file mode 100644
index 000000000..c3a0d3bec
--- /dev/null
+++ b/doc/bugs/git_annex_doesn__39__t_work_in_Max_OS_X_10.9/comment_24_c73e1277c5f284b1019362fb2bef94a8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmL8pteP2jbYJUn1M3CbeLDvz2SWAA1wtg"
+ nickname="Kristian"
+ subject="comment 24"
+ date="2013-11-17T17:01:14Z"
+ content="""
+Thanks Joey! It works great
+"""]]
diff --git a/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_11_ad13e3221ae06086e86800316912d951._comment b/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_11_ad13e3221ae06086e86800316912d951._comment
index ba2f442e4..301b0f973 100644
--- a/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_11_ad13e3221ae06086e86800316912d951._comment
+++ b/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_11_ad13e3221ae06086e86800316912d951._comment
@@ -4,7 +4,7 @@
  subject="comment 11"
  date="2013-05-19T21:13:41Z"
  content="""
-You're certianly welcome.
+You're certainly welcome.
 
 So, you did not install git-annex from the dmg? That bundles its own gpg.
 
diff --git a/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_6_7eb535ca38b3e84d44d0f8cbf5e61b8b._comment b/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_6_7eb535ca38b3e84d44d0f8cbf5e61b8b._comment
index 80a047025..03f213c43 100644
--- a/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_6_7eb535ca38b3e84d44d0f8cbf5e61b8b._comment
+++ b/doc/bugs/git_annex_fork_bombs_on_gpg_file/comment_6_7eb535ca38b3e84d44d0f8cbf5e61b8b._comment
@@ -8,7 +8,7 @@ So there are a lot of uploads attempts being made (and apparently failing), and
 
 The repeated \"(gpg)\" is an interesting clue, since normally git-annex only runs gpg once, to unlock an encrypted special remote's encryption key, and then should retain the key, cached in memory. I was able to reproduce this part of the bug (but not the zombie processes) when I purposfully broke the bup special remote by making it throw an error when it was supposed to run bup to send a file. That defeats the caching, since the state, including the cache, is thrown away when there's an exception. Working on a fix for that..
 
-That doesn't explain what's actually causing the problem for you, but it does certianly suggest the bup special remote code is failing in some unusual way. What happens if rather than starting the assistant, you use git-annex manually to send files to the remote? Run:
+That doesn't explain what's actually causing the problem for you, but it does certainly suggest the bup special remote code is failing in some unusual way. What happens if rather than starting the assistant, you use git-annex manually to send files to the remote? Run:
 
 <pre>
 git annex copy --to ffe41272-608e-43c4-8f35-e9cd63087892 --debug
diff --git a/doc/bugs/git_annex_indirect_can_fail_catastrophically.mdwn b/doc/bugs/git_annex_indirect_can_fail_catastrophically.mdwn
index 34096d894..3dc193683 100644
--- a/doc/bugs/git_annex_indirect_can_fail_catastrophically.mdwn
+++ b/doc/bugs/git_annex_indirect_can_fail_catastrophically.mdwn
@@ -70,7 +70,7 @@ index 7835988..ed8ea6c 100644
 
 Any update on this? Why is `-a` used here? -- [[anarcat]]
 
-> -a is not really the problem. You certianly do usually want
+> -a is not really the problem. You certainly do usually want
 > to commit your changes before converting to direct mode.
 > 
 > [[done]]; now when this happens it catches the exception and 
diff --git a/doc/bugs/git_version_in_prebuilt_linux_tarball_is_outdated.mdwn b/doc/bugs/git_version_in_prebuilt_linux_tarball_is_outdated.mdwn
index 8aed26bba..e5960b62e 100644
--- a/doc/bugs/git_version_in_prebuilt_linux_tarball_is_outdated.mdwn
+++ b/doc/bugs/git_version_in_prebuilt_linux_tarball_is_outdated.mdwn
@@ -6,3 +6,6 @@ Download the current prebuilt linux tarball from [[/install]], extract it, run "
 
 ### What version of git-annex are you using? On what operating system?
 git-annex-standalone-amd64.tar.gz	2013-09-22 09:56 (Linux Ubuntu Precise)
+
+> Updated to wheezy backport 1.8.4. [[done]] for now, obviously it will go
+> out of date again eventually.. --[[Joey]]
diff --git a/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files.mdwn b/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files.mdwn
new file mode 100644
index 000000000..449a99753
--- /dev/null
+++ b/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files.mdwn
@@ -0,0 +1,17 @@
+### Please describe the problem.
+
+When git-annex assistant on Android setups up the DCIM repo a .gitignore file is dropped into place which ignores .thumbnails/* . Unfortunately this doesn't match .thumbnails/.thumbdata* - I have a 700MB file which matches this pattern.
+
+I suspect that making the pattern in .gitignore just .thumbnails should resolve this.
+
+### What steps will reproduce the problem?
+
+Create a repo
+
+### What version of git-annex are you using? On what operating system?
+
+Nightly build for Android from yesterday (2013-11-16)
+
+### Please provide any additional information below.
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files/comment_1_f683ecf93e5a17c5c9c06225dbcce2a9._comment b/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files/comment_1_f683ecf93e5a17c5c9c06225dbcce2a9._comment
new file mode 100644
index 000000000..b90108bc4
--- /dev/null
+++ b/doc/bugs/gitignore_for_DCIM_on_Android_misses_some_files/comment_1_f683ecf93e5a17c5c9c06225dbcce2a9._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-16T22:45:52Z"
+ content="""
+\".thumbnails/*\" in .gitignore makes git ignore dotfiles in the directory in my testing, and according to git's own documentation.
+
+However, it is the case that subdir/.thumbnails/* are not ignored by \".thumbnails/*\", but \".thumbnails\" will indeed ignore .thumbnails directories at any point in the tree. So, I've made the change you suggested.
+
+(I also tested on android, with 1.8.4.1.559 and the assistant was able to honor the .gitignore, and did not add any files from `.thumbnails/`.)
+"""]]
diff --git a/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant.mdwn b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant.mdwn
new file mode 100644
index 000000000..1a0680c79
--- /dev/null
+++ b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant.mdwn
@@ -0,0 +1,55 @@
+### Please describe the problem.
+
+When I use the web app and try to create a remote on a remote server (via ssh connection) the assistant shows a gpg error.
+
+### What steps will reproduce the problem?
+
+1. Start the the web app using git-annex web app
+2. create a local repository
+3. create a new repository on a Remote server (Set up a repository on a remote server using ssh).
+4. provide correct server address, user, port, etc.
+
+Then gpg fails. 
+
+### What version of git-annex are you using? On what operating system?
+
+git-annex version: 4.20131106
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi TDFA CryptoHash
+key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+local repository version: unknown
+default repository version: 3
+supported repository versions: 3 4
+upgrade supported from repository versions: 0 1 2
+
+On Mac OS X 10.9 Mavericks, build 13A603.
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+[2013-11-14 21:03:47 CET] main: starting assistant version 4.20131106
+[2013-11-14 21:03:47 CET] Cronner: You should enable consistency checking to protect your data. 
+(Recording state in git...)
+(scanning...) [2013-11-14 21:03:47 CET] Watcher: Performing startup scan
+(started...) [2013-11-14 21:04:47 CET] Cronner: Consistency check in progress
+[2013-11-14 21:05:21 CET] Committer: Adding sunflower.html test.html cindy.css d3.js d3.min.js Accessors.js Essentials.js List.js Namespace.js and 6 other files
+
+(Recording state in git...)
+
+add /Users/ulli/Documents/annex/test.html (checksum...) ok
+### several similar adds removed for privacy reasons.
+ 
+[2013-11-14 21:05:22 CET] Committer: Committing changes to git
+ok
+(Recording state in git...)
+(Recording state in git...)
+14/Nov/2013:21:21:05 +0100 [Error#yesod-core] user error (gpg ["--quiet","--trust-model","always","--with-colons","--list-secret-keys","--fixed-list-mode"] exited 127) @(yesod-core-1.2.5:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+
+# End of transcript or log.
+"""]]
+
+> I've had reports from others that gpg works when installing from the
+> bundle. [[done]] --[[Joey]] 
diff --git a/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_1_7b409701c650b55b3472accd70555f16._comment b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_1_7b409701c650b55b3472accd70555f16._comment
new file mode 100644
index 000000000..7b1ed7420
--- /dev/null
+++ b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_1_7b409701c650b55b3472accd70555f16._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="Easy to fix."
+ date="2013-11-14T20:36:17Z"
+ content="""
+Well, this only happens when gpg is not available. Everything works fine after a quick \"brew install gpg\".
+"""]]
diff --git a/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_2_40b00f7258512677516ec5036b89090f._comment b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_2_40b00f7258512677516ec5036b89090f._comment
new file mode 100644
index 000000000..ecc9717d2
--- /dev/null
+++ b/doc/bugs/gpg_fails_on_Mac_OS_10.9_when_creating_a_new_remote_repository_via_assistant/comment_2_40b00f7258512677516ec5036b89090f._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 2"
+ date="2013-11-14T22:10:32Z"
+ content="""
+gpg is included in the bundle though:
+
+<pre>
+oberon:tmp joeyh$ /Volumes/git-annex/git-annex.app/Contents/MacOS/runshell
+bash-3.2$ which gpg
+/Volumes/git-annex/git-annex.app/Contents/MacOS/bundle/gpg
+</pre>
+"""]]
diff --git a/doc/bugs/importfeed_should_allow_pubdate_in_the_template.mdwn b/doc/bugs/importfeed_should_allow_pubdate_in_the_template.mdwn
new file mode 100644
index 000000000..44d25b02d
--- /dev/null
+++ b/doc/bugs/importfeed_should_allow_pubdate_in_the_template.mdwn
@@ -0,0 +1,5 @@
+importfeed is a great feature, but it doesn't allow templating the filename with the publish date.
+
+I would suggest adding pubdate option, which would fix this problem.
+
+> duplicate of [[todo/importfeed: allow ${itemdate} with --template]] [[done]] --[[Joey]] 
diff --git a/doc/bugs/internal_server_error:_hGetContents:_invalid_argument___40__invalid_byte_sequence__41__.mdwn b/doc/bugs/internal_server_error:_hGetContents:_invalid_argument___40__invalid_byte_sequence__41__.mdwn
new file mode 100644
index 000000000..8c9703ed2
--- /dev/null
+++ b/doc/bugs/internal_server_error:_hGetContents:_invalid_argument___40__invalid_byte_sequence__41__.mdwn
@@ -0,0 +1,29 @@
+### Please describe the problem.
+
+Some logs fail to be displayed, and instead of displaying parts of the log, no logs at all are displayed in the webapp.
+
+The problem character is, I believe, a latin-1 encoded filename (as opposed to UTF-8). --[[anarcat]]
+
+### What steps will reproduce the problem?
+
+1. download [this logfile](http://paste.anarc.at/daemon.log.1)
+2. install it in .git/annex/daemon.log
+3. load the webapp
+4. visit the logs page
+
+### What version of git-annex are you using? On what operating system?
+
+4.20131105-g8efdc1a
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+Internal Server Error
+/srv/video/.git/annex/daemon.log.1: hGetContents: invalid argument (invalid byte sequence)
+git-annex version 4.20131105-g8efdc1a
+# End of transcript or log.
+"""]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/internal_server_error:_unknown_UUID_on_webapp.mdwn b/doc/bugs/internal_server_error:_unknown_UUID_on_webapp.mdwn
new file mode 100644
index 000000000..307eed308
--- /dev/null
+++ b/doc/bugs/internal_server_error:_unknown_UUID_on_webapp.mdwn
@@ -0,0 +1,147 @@
+### Please describe the problem.
+
+I am having trouble using the webapp with a setup I did on the commandline that was working fine.
+
+I have two machines: one, a server called `marcos`, is available on the internetz and I cloned a repo from there into `markov`, a workstation that is hidden behind a NAT connexion (so I can't add it as a remote).
+
+It seems that because the remote is not locally available as a git remote, the webapp is freaking out because it doesn't recognize `markov` as a proper remote.
+
+### What steps will reproduce the problem?
+
+1. setup git annex locally (on `marcos`) in a repository (probably `git annex init; git annex direct; git annex add .` i somewhat followed [[tips/Git_annex_and_Calibre/]])
+2. `git clone` that repo on a remote, unaccessible (NAT'd) server (`markov`)
+3. start doing some git annex get, get tired, run the web app on `markov`
+4. let that run over there, go back to `marcos`
+5. be curious about what is going on on `markov`, run the webapp and enter the path to the repository created in step one when prompted (it's the first time i run the webapp)
+6. it starts up fine, but doesn't seem to detect `markov`, marking transfers as going to the remote named `unknown`
+7. click on the `unknown` link, crash
+8. go back to the dashboard, crash
+
+From there on, the webapp is pretty much crashed, starting it from scratch asks me if i want to create a git annex repo.
+
+### What version of git-annex are you using? On what operating system?
+
+4.20130921-gd4739c5 compiled and installed by hand on debian wheezy.
+
+### Please provide any additional information below.
+
+[[!format sh """
+# Here's everything that has been logged by the git-annex assistant, as well as by programs it has run.
+
+[2013-11-04 22:42:50 EST] main: starting assistant version 4.20130921-gd4739c5
+(merging synced/git-annex into git-annex...)
+(Recording state in git...)
+
+  No known network monitor available through dbus; falling back to polling
+Already up-to-date.
+
+(scanning...) [2013-11-04 22:42:50 EST] Watcher: Performing startup scan
+04/Nov/2013:22:42:51 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:42:52 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:42:52 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+(Recording state in git...)
+(Recording state in git...)
+(started...) 
+
+  metadata.db still has writers, not adding
+[2013-11-04 22:42:59 EST] Committer: Adding cover.jpg Ars Techn..ibre.epub Cyberpres..ibre.epub cover.jpg cover.jpg Ars Techn..ibre.epub cover.jpg Democracy..ibre.epub cover.jpg and 11 other files
+add Calibre/Ars Technica [dim., 03 nov. 2013] (645)/cover.jpg (checksum...) ok
+add Calibre/Ars Technica [dim., 03 nov. 2013] (645)/Ars Technica [dim., 03 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Cyberpresse [lun., 04 nov. 2013] (647)/Cyberpresse [lun., 04 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Cyberpresse [lun., 04 nov. 2013] (647)/cover.jpg (checksum...) ok
+add Calibre/Ars Technica [sam., 02 nov. 2013] (642)/cover.jpg (checksum...) ok
+add Calibre/Ars Technica [sam., 02 nov. 2013] (642)/Ars Technica [sam., 02 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Democracy now! [lun., 04 nov. 2013] (649)/cover.jpg (checksum...) ok
+add Calibre/Democracy now! [lun., 04 nov. 2013] (649)/Democracy now! [lun., 04 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/xkcd [lun., 04 nov. 2013] (646)/cover.jpg (checksum...) ok
+add Calibre/xkcd [lun., 04 nov. 2013] (646)/xkcd [lun., 04 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Cyberpresse [dim., 03 nov. 2013] (644)/cover.jpg (checksum...) ok
+add Calibre/Cyberpresse [dim., 03 nov. 2013] (644)/Cyberpresse [dim., 03 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Le Devoir [sam., 02 nov., 2013] (640)/cover.jpg (checksum...) ok
+add Calibre/Le Devoir [sam., 02 nov., 2013] (640)/Le Devoir [sam., 02 nov., 2013] - Calibre.epub (checksum...) ok
+add Calibre/Le Devoir [lun., 04 nov., 2013] (648)/cover.jpg (checksum...) ok
+add Calibre/Le Devoir [lun., 04 nov., 2013] (648)/Le Devoir [lun., 04 nov., 2013] - Calibre.epub (checksum...) ok
+add Calibre/Cyberpresse [sam., 02 nov. 2013] (641)/cover.jpg (checksum...) ok
+add Calibre/Cyberpresse [sam., 02 nov. 2013] (641)/Cyberpresse [sam., 02 nov. 2013] - Calibre.epub (checksum...) ok
+add Calibre/Le Devoir [dim., 03 nov., 2013] (643)/cover.jpg (checksum...) ok
+add Calibre/Le Devoir [dim., 03 nov., 2013] (643)/Le Devoir [dim., 03 nov., 2013] - Calibre.epub (checksum...) [2013-11-04 22:43:01 EST] Committer: Committing changes to git
+ok
+(Recording state in git...)
+(Recording state in git...)
+04/Nov/2013:22:43:51 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:47:24 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:47:24 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:47:24 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:52:29 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:52:30 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:52:30 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:56:47 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+[2013-11-04 22:57:08 EST] Committer: Adding metadata.db-journal
+add metadata.db-journal (checksum...) [2013-11-04 22:57:08 EST] Committer: Committing changes to git
+[2013-11-04 22:57:09 EST] Committer: Adding metadata.db-journal metadata.db
+ok
+(Recording state in git...)
+(Recording state in git...)
+add metadata.db (checksum...) [2013-11-04 22:57:09 EST] Committer: Committing changes to git
+ok
+(Recording state in git...)
+(Recording state in git...)
+04/Nov/2013:22:57:12 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:57:15 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:57:18 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+04/Nov/2013:22:57:20 -0500 [Error#yesod-core] Unknown UUID @(yesod-core-1.2.4.2:Yesod.Core.Class.Yesod ./Yesod/Core/Class/Yesod.hs:485:5)
+"""]]
+
+> I wonder if this couldn't be related to [[cannot determine uuid for origin]], although in this case the remote is just not added to `.git/config`. --[[anarcat]]
+
+> This was fixed in commit 44e1524be53373ddbf28d643bedf5455433c2b2e
+> on Sep 29th. You should update. [[done]]
+> 
+> (It also sounds like your repository on markov is for some reason not
+> able to push its git repository to marcos. You might need to fix
+> something in your setup to get syncing working) --[[Joey]]
+> 
+> > Humm.. Weird. Upgrading fixes the crash, but `marcos` still sees only
+> > one repository. It sees some syncs going on from `unknown`, and when
+> > I click on that `unknown` link, I get to edit that repository, and
+> > it sees it as `here`. So I am not sure I understand what is going 
+> > on here.
+> >
+> > (As for the repo on `markov`, it does sync properly:
+> > 
+> >     anarcat@desktop008:books$ git annex sync
+> >     commit
+> >     ok
+> >     pull origin
+> >     From anarc.at:/srv/books
+> >        3b4fa7b..c35b13e  git-annex  -> origin/git-annex
+> >     ok
+> > 
+> > Or rather - it doesn't fail. But it doesn't push!
+> > 
+> >     anarcat@desktop008:books$ git push
+> >     Everything up-to-date
+> > 
+> > Note that git on `marcos` is the 1.8.4 backport for some reason.
+> > I know that branch tracking changed with that release, maybe 
+> > that's the problem? --[[anarcat]])
+> > 
+> > > So yep, I confirm that even in 4.20131105-g8efdc1a, the webapp
+> > > doesn't find the `markov` remote properly, even though
+> > > `git annex status` can:
+> > > 
+> > >     $ git annex status
+> > >     repository mode: direct
+> > >     trusted repositories: 0
+> > >     semitrusted repositories: 3
+> > >             00000000-0000-0000-0000-000000000001 -- web
+> > >             a75cbbf7-e055-423e-b375-443e0552c9e2 -- here (anarcat@marcos:/srv/books)
+> > >             aa500f29-42d9-4777-ae02-4a2c3d47db44 -- anarcat@markov:~/books
+> > > 
+> > > I see transfers happening, but they go to "unknown". The link is:
+> > > 
+> > > http://127.0.0.1:56577/config/repository/edit/UUID%20%22aa500f29-42d9-4777-ae02-4a2c3d47db44%22?auth=...
+> > > 
+> > > -- [[anarcat]]
+> > > 
+> > > > I have filed this as a separate bug to close the discussion properly here, sorry for the noise. :) see [[bugs/remote_not_showing_up_in_webapp]] --[[anarcat]]
diff --git a/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_2_926a87b60e20d286d49639c8dad13a1a._comment b/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_2_926a87b60e20d286d49639c8dad13a1a._comment
new file mode 100644
index 000000000..878e8fd7d
--- /dev/null
+++ b/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_2_926a87b60e20d286d49639c8dad13a1a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="correlation does not imply causation"
+ date="2013-11-01T16:37:31Z"
+ content="""
+I've been using git-annex on thumbdrives for years without problems. It seems more likely to me that you have a general problem with your hardware than that one program that does nothing special is somehow at fault.
+"""]]
diff --git a/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_3_c509fba1a9adacfd26a2bd12b4aea988._comment b/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_3_c509fba1a9adacfd26a2bd12b4aea988._comment
new file mode 100644
index 000000000..01ab119d2
--- /dev/null
+++ b/doc/bugs/microsd__47__thumbdrives_seem_to_die_when_using_the_ARM_build/comment_3_c509fba1a9adacfd26a2bd12b4aea988._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
+ nickname="Carlo"
+ subject="comment 3"
+ date="2013-11-02T17:29:55Z"
+ content="""
+True, and good to know. Didn't necessarily want to trigger a big bug hunt here anyway, just some data/logs in case any more correlation comes up.
+"""]]
diff --git a/doc/bugs/non-repos_in_repositories_list___40__+_other_weird_output__41___from_git_annex_status/comment_4_d0e55585f1612148163039d157253258._comment b/doc/bugs/non-repos_in_repositories_list___40__+_other_weird_output__41___from_git_annex_status/comment_4_d0e55585f1612148163039d157253258._comment
index dccc5cd6a..1e2a8fe24 100644
--- a/doc/bugs/non-repos_in_repositories_list___40__+_other_weird_output__41___from_git_annex_status/comment_4_d0e55585f1612148163039d157253258._comment
+++ b/doc/bugs/non-repos_in_repositories_list___40__+_other_weird_output__41___from_git_annex_status/comment_4_d0e55585f1612148163039d157253258._comment
@@ -4,7 +4,7 @@
  subject="comment 4"
  date="2013-07-26T16:52:26Z"
  content="""
-The 4201 dangling blobs is a little bit strange, although it could certianly happen in some normal scenarios.
+The 4201 dangling blobs is a little bit strange, although it could certainly happen in some normal scenarios.
 Overall, your repository seems to be ok except for this weird data in the one file. I do not anticipate the extra garbage causing any problems at all.
 
 To track this down, we need to find the commit that added the garbage. One way, assuming you're using indirect mode, is to `git checkout git-annex; git blame uuid.log` and `git show` the commit that added the garbage. If you're using direct mode, you should first `git clone` the repository and do that in the clone.
diff --git a/doc/bugs/remote_not_showing_up_in_webapp.mdwn b/doc/bugs/remote_not_showing_up_in_webapp.mdwn
new file mode 100644
index 000000000..f8b4da7b1
--- /dev/null
+++ b/doc/bugs/remote_not_showing_up_in_webapp.mdwn
@@ -0,0 +1,88 @@
+### Please describe the problem.
+
+This is a followup on [[bugs/internal_server_error:_unknown_UUID_on_webapp]]. In that issue, webapps previous to 20130929 would crash with `internal server error: unknown UUID`. This was fixed at that date, but some problems remain, namely that the remote that is recognized on the commandline doesn't show up in the webapp.
+
+`markov` is able to push to `marcos`, but not the reverse because `markov` is hidden behind a NAT. `git annex sync` seems to do the right thing accordingly on both ends (which is: `marcos` doesn't try to push to `markov` but `markov` pushes to `marcos`).
+
+### What steps will reproduce the problem?
+
+See [[bugs/internal_server_error:_unknown_UUID_on_webapp]]. I didn't do any further changes other than upgrade `git-annex` on both ends.
+
+### What version of git-annex are you using? On what operating system?
+
+`marcos` is now running `Version: 4.20131105-g8efdc1a Build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi TDFA CryptoHash`
+
+`markov` is now running the wheezy backport, `4.20131002~bpo70+1`.
+
+### Please provide any additional information below.
+
+#### On `marcos`
+
+Here's the output of `git annex status` on `marcos`:
+
+[[!format sh """
+anarcat@marcos:books$ git annex status
+repository mode: direct
+trusted repositories: 0
+semitrusted repositories: 3
+        00000000-0000-0000-0000-000000000001 -- web
+        a75cbbf7-e055-423e-b375-443e0552c9e2 -- here (anarcat@marcos:/srv/books)
+        aa500f29-42d9-4777-ae02-4a2c3d47db44 -- anarcat@markov:~/books
+untrusted repositories: 0
+transfers in progress: none
+available local disk space: 7.04 gigabytes (+1 megabyte reserved)
+local annex keys: 736
+local annex size: 3.92 gigabytes
+annexed files in working tree: 721
+size of annexed files in working tree: 3.92 gigabytes
+bloom filter size: 16 mebibytes (0.1% full)
+backend usage:
+        SHA256E: 1457
+# End of transcript or log.
+"""]]
+
+Here's a screenshot of the idle webapp on marcos:
+
+<img src="http://i.imgur.com/3HFgj3w.png" />
+
+You can clearly see that the webapp doesn't see the `markov` remote.
+
+When `markov` transfers stuff, `marcos` sees the transfers happening, but marks it as going to the `unknown` remote:
+
+<img src="http://i.imgur.com/YOu9GbA.png" />
+
+Clicking on that link is what was previously triggering [[bugs/internal_server_error:_unknown_UUID_on_webapp]] but now yields a "Unknown remote" error.
+
+<img src="http://i.imgur.com/y7JxULi.png" />
+
+#### On `markov`:
+
+Here is a screenshot from `markov` that shows *it* knows about both repositories and seem to behave properly:
+
+<img src="http://i.imgur.com/fTMslVT.png" />
+
+And here's the output of `git annex status` on markov:
+
+[[!format sh """
+anarcat@desktop008:books$ git annex status
+repository mode: indirect
+trusted repositories: 0
+semitrusted repositories: 3
+        00000000-0000-0000-0000-000000000001 -- web
+        a75cbbf7-e055-423e-b375-443e0552c9e2 -- origin (anarcat@marcos:/srv/books)
+        aa500f29-42d9-4777-ae02-4a2c3d47db44 -- here (anarcat@markov:~/books)
+untrusted repositories: 0
+transfers in progress:
+        downloading Patrick K. O'Brien/Philip's Atlas of World History, Concise Edition (115)/Philip's Atlas of World History, Concise Edition - Patrick K. O'Brien.pdf from origin
+available local disk space: 93.25 gigabytes (+1 megabyte reserved)
+temporary directory size: 50.07 megabytes (clean up with git-annex unused)
+local annex keys: 708
+local annex size: 3.81 gigabytes
+known annex keys: 721
+known annex size: 3.92 gigabytes
+bloom filter size: 16 mebibytes (0.1% full)
+backend usage:
+        SHA256E: 1429
+"""]]
+
+Finally, note that you sometimes see `desktop008` above: it turns out I am running `git annex` from my workstation, which NFS-mounts the `/home` directory of `markov` into `/srv/musique`.  --[[anarcat]]
diff --git a/doc/bugs/remote_not_showing_up_in_webapp/comment_1_2a269732fd528f505777542d3556437a._comment b/doc/bugs/remote_not_showing_up_in_webapp/comment_1_2a269732fd528f505777542d3556437a._comment
new file mode 100644
index 000000000..4582a3071
--- /dev/null
+++ b/doc/bugs/remote_not_showing_up_in_webapp/comment_1_2a269732fd528f505777542d3556437a._comment
@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-06T16:38:47Z"
+ content="""
+marcov does not show up in the webapp because there is no configured git remote for it.
+
+This is a slightly confusing corner of the webapp. The webapp will show repositories that do not have a configured remote, but it only does it for special remotes. ssh repos, being regular git remotes, don't currently show up in the webapp unless that repository is actually set up as a remote.
+
+It should certainly not show it as \"unknown\"; it would be much better to use the full repo description here, since it does not have a remote name.
+(Unless the description is really long!)
+
+I think you'll also get the \"unknown uuid\" screen even for a special remote that is not configured in the local repository. So that needs to be fixed.
+
+Finally, it would probably be good for the webapp to show ssh repos that don't have remotes as existing, and let the user enter a ssh address to configure them. The problem with trying to do this is it actually has no idea that this is a ssh repo. It could just as easily be a local directory. The UI to configure  it would be pretty elaborate.
+"""]]
diff --git a/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_2_93af8f48a01b6e2d011bd6f60499ccd2._comment b/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_2_93af8f48a01b6e2d011bd6f60499ccd2._comment
new file mode 100644
index 000000000..a0e73cc5e
--- /dev/null
+++ b/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_2_93af8f48a01b6e2d011bd6f60499ccd2._comment
@@ -0,0 +1,23 @@
+[[!comment format=mdwn
+ username="http://nicolas-schodet.myopenid.com/"
+ ip="81.56.19.53"
+ subject="comment 2"
+ date="2013-11-23T14:38:21Z"
+ content="""
+Here are the files in details:
+
+[[!format sh \"\"\"
+Umba:.../.git$ ls -ld $(find . -name SHA256-s2819887-\*) # the bad file
+drwxr-xr-t  4 marie-eve  staff  136 Aug 17 17:05 ./annex/objects/wq/3j/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c/
+-rw-r--r--  1 marie-eve  staff  560 Nov 23 15:25 ./annex/objects/wq/3j/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c.cache
+-rw-------  1 marie-eve  staff   33 Aug 17 17:05 ./annex/objects/wq/3j/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c.map
+-rw-r--r--  1 marie-eve  staff   52 Aug 17 17:06 ./annex/transfer/failed/download/13fd5d5a-ed97-11e2-9178-574d3b1c0618/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c
+-rw-r--r--  1 marie-eve  staff   51 Aug 17 10:13 ./annex/transfer/failed/download/95443f2e-ed96-11e2-9d3f-8ffa5b1aae7a/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c
+Umba:.../.git$ ls -ld $(find . -name SHA256-s5066556-\*) # a good file
+dr-xr-xr-x  3 marie-eve  staff      102 Nov 23 15:27 ./annex/objects/Fx/w0/SHA256-s5066556--0e4a47efdc14c884d07c017ba5506a56affb136d87bef5700145774fd9089f25/
+-r--r--r--  1 marie-eve  staff  5066556 Nov  6 17:43 ./annex/objects/Fx/w0/SHA256-s5066556--0e4a47efdc14c884d07c017ba5506a56affb136d87bef5700145774fd9089f25/SHA256-s5066556--0e4a47efdc14c884d07c017ba5506a56affb136d87bef5700145774fd9089
+Umba:.../.git$
+\"\"\"]]
+
+No more idea on how it reached this situation.
+"""]]
diff --git a/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_3_f8fba1955e62360061613e5898b3d74e._comment b/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_3_f8fba1955e62360061613e5898b3d74e._comment
new file mode 100644
index 000000000..d7d05da85
--- /dev/null
+++ b/doc/bugs/rename:_permission_denied__44___after_direct_mode_switch/comment_3_f8fba1955e62360061613e5898b3d74e._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="http://nicolas-schodet.myopenid.com/"
+ ip="81.56.19.53"
+ subject="comment 3"
+ date="2013-11-23T15:42:26Z"
+ content="""
+The link seems to be special:
+
+[[!format sh \"\"\"
+Umba:2013-07-31$ ls -lO 2013-07-31_180411.jpg 
+lrwxr-xr-x  1 marie-eve  staff  uchg 191 Aug 12 21:45 2013-07-31_180411.jpg@ -> ../.git/annex/objects/wq/3j/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c/SHA256-s2819887--987f9811d7b5c7a287a74b7adbb852be4d18eeda61c3507f4e08c534d2356f4c
+Umba:2013-07-31$
+\"\"\"]]
+
+I tried the chflags command with no success... I suppose I need a MAC specialist.
+"""]]
diff --git a/doc/bugs/repair_fails_when_home_on_seperate_partition.mdwn b/doc/bugs/repair_fails_when_home_on_seperate_partition.mdwn
new file mode 100644
index 000000000..19780c7de
--- /dev/null
+++ b/doc/bugs/repair_fails_when_home_on_seperate_partition.mdwn
@@ -0,0 +1,60 @@
+### Please describe the problem.
+
+
+### What steps will reproduce the problem?
+
+(1) Place a broken repo on a different mount point than the root partition.
+
+(2) Run
+    git annex repair.
+
+### What version of git-annex are you using? On what operating system?
+
+ 5.20131118-gc7e5cde on Ubuntu 12.04
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+$ git annex repair --force
+
+Running git fsck ...
+git fsck found 74 broken objects.
+Unpacking all pack files.
+Unpacking objects: 100% (2307/2307), done.
+Unpacking objects: 100% (241565/241565), done.
+Re-running git fsck to see if it finds more problems.
+Initialized empty Git repository in /tmp/tmprepo.0/.git/
+Trying to recover missing objects from remote pi.fritz.box__var_lib_store_annex
+Trying to recover missing objects from remote pi.fritz.box__var_lib_store_annex
+74 missing objects could not be recovered!
+
+
+Deleted remote branch pi.fritz.box__var_lib_store_annex/master (was dffa056).
+error: Could not read 4e01bbdc7ce31247ad66ab13ca46925ac2c8db9a
+fatal: Failed to traverse parents of commit 718525a48b4d6b3404eda5e189332d73c968a2be
+Deleted remote branch pi.fritz.box__var_lib_store_annex/synced/git-annex (was 718525a).
+Deleted remote branch pi.fritz.box__var_lib_store_annex/synced/master (was 9aedf69).
+Deleted remote branch pi.fritz.box_annex/synced/master (was 92b1042).
+Deleted remote branch store/master (was b059380).
+removed 5 remote tracking branches that referred to missing objects
+fatal: bad object refs/heads/git-annex
+fatal: bad object refs/heads/git-annex
+fatal: bad object refs/heads/git-annex
+error: remote branch 'git-annex' not found.
+
+git-annex: /tmp/packed-refs19813: rename: unsupported operation (Invalid cross-device link)
+failed
+git-annex: repair: 1 failed
+
+
+# End of transcript or log.
+"""]]
+
+> Thanks for reporting. As far as I can see, this was fixed
+> accidentially, when I rewrote the packed refs file handling code to not
+> re-write the file. It had been using a temp file, and renaming it, thus
+> the problem. I checked the repair code and can find no other probems
+> of this sort currently in it. [[done]] --[[Joey]]
diff --git a/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink.mdwn b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink.mdwn
new file mode 100644
index 000000000..3f8c7fc48
--- /dev/null
+++ b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink.mdwn
@@ -0,0 +1,41 @@
+### Please describe the problem.
+
+ATM git annex assistant app is the largest one installed on my phone.  I simply keep hitting the available storage space limits and keep pruning some apps
+
+According to file
+$> file lib/armeabi/lib.git-annex.so
+lib/armeabi/lib.git-annex.so: ELF 32-bit LSB  executable, ARM, EABI5 version 1 (SYSV), dynamically linked (uses shared libs), not stripped
+so largest annex's .so is 133M and is not stripped.  stripping it seems to half its size: 
+
+$> ls -l lib.git-annex.so 
+62052 -rw------- 1 yoh yoh 63468304 Nov 25 22:21 lib.git-annex.so
+$> file lib.git-annex.so
+lib.git-annex.so: ELF 32-bit LSB executable, ARM, version 1 (SYSV), dynamically linked (uses shared libs), stripped
+
+so may be it could be the first step to make the .apk and installation itself more lightweight and thus easier to "manage"
+
+thanks in advance
+
+### What steps will reproduce the problem?
+
+install provided .apk on Android
+
+### What version of git-annex are you using? On what operating system?
+
+Android, just fetched the most recent "release" apk from the
+http://downloads.kitenet.net/git-annex/android/current/4.0/git-annex.apk
+Last-Modified: Mon, 18 Nov 2013 11:57:25 GMT
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+
+# End of transcript or log.
+"""]]
+
+> Seems that I lost stripping of the git-annex binary when adding the build
+> for the newer android versions. [[fixed|done]] (There is not otherwise
+> much way to shrink the size.) --[[Joey]]
diff --git a/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_1_d2faaff98386433110dcf7aae87916b7._comment b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_1_d2faaff98386433110dcf7aae87916b7._comment
new file mode 100644
index 000000000..894c48784
--- /dev/null
+++ b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_1_d2faaff98386433110dcf7aae87916b7._comment
@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="http://yarikoptic.myopenid.com/"
+ nickname="site-myopenid"
+ subject="sure there is no other ways to shrink?"
+ date="2013-11-27T04:26:35Z"
+ content="""
+Might be quite a stretch but it is hard to grasp that all 60MB are really needed... although with haskell -- it might indeed be the case, but I thought that may be there could be some symbols pulled in which aren't used, and for which when in gcc/ld world there are ways to get rid of them, e.g. -dead_strip (just excercising ideas)
+
+"""]]
diff --git a/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_2_1359ddf1b5db4303f8bd219d3f07df3a._comment b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_2_1359ddf1b5db4303f8bd219d3f07df3a._comment
new file mode 100644
index 000000000..5f7688d1f
--- /dev/null
+++ b/doc/bugs/size_of_the_Android_installation_is_HUGE_--_please_seek_possibility_to_shrink/comment_2_1359ddf1b5db4303f8bd219d3f07df3a._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 2"
+ date="2013-11-27T04:55:51Z"
+ content="""
+The git-annex binary is around 45 mb on Linux. The android binary statically links a few additional C libraries, so is slightly larger.
+
+The only way I know of to potentially shrink it is to fix certian ghc / ld interactions that, in my limited understanding, cause functions that are never used to be linked into the binary if another function in the same file (or module) is used. That might half its size or something.
+"""]]
diff --git a/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo.mdwn b/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo.mdwn
index 671041e67..3aa3188af 100644
--- a/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo.mdwn
+++ b/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo.mdwn
@@ -40,3 +40,5 @@ ssh-keygen: symbol lookup error: /lib64/libldap-2.4.so.2: undefined symbol: ber_
 
 # End of transcript or log.
 """]]
+
+> Added ssh-keygen to bundle. [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo/comment_1_52180983b59c247389a55a9523ec435b._comment b/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo/comment_1_52180983b59c247389a55a9523ec435b._comment
new file mode 100644
index 000000000..f0f50151a
--- /dev/null
+++ b/doc/bugs/ssh-keygen_failed_when_adding_remote_server_repo/comment_1_52180983b59c247389a55a9523ec435b._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 1"
+ date="2013-11-08T18:28:37Z"
+ content="""
+Apologies for not following up on this bug sooner..
+
+It seems to me that your system has a broken ssh-keygen program. You didn't say how you installed git-annex, but based on the git rev in the version number, I'm guessing you either built it yourself, or you're using the standalone tarball I build.
+
+In the case of the latter, it didn't include ssh-keygen, so would try to use the one that comes with fedora. It seems likely that the problem comes from the libraries included in the bundle being used with a binary not in the bundle, that in turn is also using additional libraries.
+
+So, I think I should add ssh-keygen to the standalone bundle!
+"""]]
diff --git a/doc/bugs/test_failures_on_window_for_5.20131118.mdwn b/doc/bugs/test_failures_on_window_for_5.20131118.mdwn
new file mode 100644
index 000000000..490bdf2c8
--- /dev/null
+++ b/doc/bugs/test_failures_on_window_for_5.20131118.mdwn
@@ -0,0 +1,20 @@
+### Please describe the problem.
+
+git annex test reports failures
+
+### What steps will reproduce the problem?
+
+running git annex test (from standard cmd, with: git version: 1.7.11.msysgit.1)
+
+### What version of git-annex are you using? On what operating system?
+
+5.20131118 from installers
+
+### Please provide any additional information below.
+
+operating system:
+
+windows XP, NTFS = 1 FAIL
+windows 7, NTFS = 2 FAILs
+
+see attachment for full log of git annex test output
diff --git a/doc/bugs/test_failures_on_window_for_5.20131118/comment_1_5a7a284625c12d54390fe4a4ec1d4211._comment b/doc/bugs/test_failures_on_window_for_5.20131118/comment_1_5a7a284625c12d54390fe4a4ec1d4211._comment
new file mode 100644
index 000000000..d27e69b30
--- /dev/null
+++ b/doc/bugs/test_failures_on_window_for_5.20131118/comment_1_5a7a284625c12d54390fe4a4ec1d4211._comment
@@ -0,0 +1,188 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkJafmCf-sg9_OM0pynFYM3AO4WCgJiaMI"
+ nickname="Michele"
+ subject="seems i'm not allowed to attach full logs."
+ date="2013-11-23T16:06:17Z"
+ content="""
+here's an excerpt (the context of FAIL), hopefully i've interpreted correctely the test begin message.
+
+win7:
+
+        unannex (with copy):                              Detected a filesystem without fifo support.
+  Disabling ssh connection caching.
+  Detected a crippled filesystem.
+  Enabling direct mode.
+get foo (merging origin/git-annex into git-annex...)
+(Recording state in git...)
+(from origin...) 
+foo
+          20 100%    0.00kB/s    0:00:00
+          20 100%    0.00kB/s    0:00:00 (xfer#1, to-check=0/1)
+
+sent 87 bytes  received 31 bytes  236.00 bytes/sec
+total size is 20  speedup is 0.17
+ok
+(Recording state in git...)
+unannex foo 
+git-annex: M:\gitannex.test\.t\tmprepo4\.git\annex\objects\6cd\e82\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77.map4432.tmp: MoveFileEx \"M:\\gitannex.test\\.t\\tmprepo4\\.git\\annex\\objects\\6cd\\e82\\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77\\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77.map4432.tmp\" \"M:\\gitannex.test\\.t\\tmprepo4\\.git\\annex\\objects\\6cd\\e82\\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77\\SHA256E-s20--e394a389d787383843decc5d3d99b6d184ffa5fddeec23b911f9ee7fc8b9ea77.map\": permission denied (Access is denied.)
+failed
+git-annex: unannex: 1 failed
+FAIL
+
+		conflict_resolution (mixed directory and file):   Detected a filesystem without fifo support.
+	  Disabling ssh connection caching.
+	  Detected a crippled filesystem.
+	  Enabling direct mode.
+	  Detected a filesystem without fifo support.
+	  Disabling ssh connection caching.
+	  Detected a crippled filesystem.
+	  Enabling direct mode.
+	add conflictor (checksum...) ok
+	(Recording state in git...)
+	(merging origin/git-annex origin/synced/git-annex into git-annex...)
+	(Recording state in git...)
+	commit  
+	ok
+	pull origin bash.exe: warning: could not find /tmp, please create!
+
+	ok
+	push origin bash.exe: warning: could not find /tmp, please create!
+	To M:/gitannex.test/.t\repo
+	   32fb7c0..38147e0  git-annex -> synced/git-annex
+	   7684984..4116595  annex/direct/master -> synced/master
+
+	ok
+	add conflictor/subfile (checksum...) ok
+	(Recording state in git...)
+	(merging origin/git-annex origin/synced/git-annex into git-annex...)
+	(Recording state in git...)
+	commit  
+	ok
+	pull origin bash.exe: warning: could not find /tmp, please create!
+	From M:/gitannex.test/.t\repo
+	   7684984..4116595  master     -> origin/master
+	   32fb7c0..38147e0  synced/git-annex -> origin/synced/git-annex
+	   7684984..4116595  synced/master -> origin/synced/master
+	Adding conflictor/subfile
+	CONFLICT (directory/file): There is a directory with name conflictor in HEAD. Adding conflictor as conflictor~refs_remotes_origin_synced_master
+	Automatic merge failed; fix conflicts and then commit the result.
+	Ignoring path ./conflictor.variant-cc12
+	conflictor: needs merge
+	[annex/direct/master 27c52e4] git-annex automatic merge conflict fix
+
+
+	(Recording state in git...)
+
+	  Merge conflict was automatically resolved; you may want to examine the result.
+	ok
+	(merging origin/synced/git-annex into git-annex...)
+	(Recording state in git...)
+	push origin bash.exe: warning: could not find /tmp, please create!
+	To M:/gitannex.test/.t\repo
+	   38147e0..02916ee  git-annex -> synced/git-annex
+	   4116595..27c52e4  annex/direct/master -> synced/master
+
+	ok
+	commit  
+	ok
+	pull r2 bash.exe: warning: could not find /tmp, please create!
+	From ../../.t\tmprepo35
+	 * [new branch]      annex/direct/master -> r2/annex/direct/master
+	 * [new branch]      git-annex  -> r2/git-annex
+	 * [new branch]      master     -> r2/master
+	 * [new branch]      synced/master -> r2/synced/master
+	Updating 4116595..27c52e4
+	Fast-forward
+	 conflictor         | 1 -
+	 conflictor/subfile | 1 +
+	 2 files changed, 1 insertion(+), 1 deletion(-)
+	 delete mode 120000 conflictor
+	 create mode 120000 conflictor/subfile
+	Already up-to-date.
+
+
+
+	ok
+	(merging r2/git-annex into git-annex...)
+	FAIL
+
+
+windowsXP:
+
+    conflict_resolution (mixed directory and file):   Detected a filesystem without fifo support.
+  Disabling ssh connection caching.
+  Detected a crippled filesystem.
+  Enabling direct mode.
+  Detected a filesystem without fifo support.
+  Disabling ssh connection caching.
+  Detected a crippled filesystem.
+  Enabling direct mode.
+add conflictor (checksum...) ok
+(Recording state in git...)
+(merging origin/git-annex origin/synced/git-annex into git-annex...)
+(Recording state in git...)
+commit  
+ok
+pull origin bash.exe: warning: could not find /tmp, please create!
+
+ok
+push origin bash.exe: warning: could not find /tmp, please create!
+To C:/Documents and Settings/Silvia/.t\repo
+   edd69f1..83c6a5a  git-annex -> synced/git-annex
+   bed393e..978ac14  annex/direct/master -> synced/master
+
+ok
+add conflictor/subfile (checksum...) ok
+(Recording state in git...)
+(merging origin/git-annex origin/synced/git-annex into git-annex...)
+(Recording state in git...)
+commit  
+ok
+pull origin bash.exe: warning: could not find /tmp, please create!
+From C:/Documents and Settings/Silvia/.t\repo
+   bed393e..978ac14  master     -> origin/master
+   edd69f1..83c6a5a  synced/git-annex -> origin/synced/git-annex
+   bed393e..978ac14  synced/master -> origin/synced/master
+Adding conflictor/subfile
+CONFLICT (directory/file): There is a directory with name conflictor in HEAD. Adding conflictor as conflictor~refs_remotes_origin_synced_master
+Automatic merge failed; fix conflicts and then commit the result.
+Ignoring path ./conflictor.variant-cc12
+conflictor: needs merge
+[annex/direct/master e3e39fc] git-annex automatic merge conflict fix
+
+
+(Recording state in git...)
+
+  Merge conflict was automatically resolved; you may want to examine the result.
+ok
+(merging origin/synced/git-annex into git-annex...)
+(Recording state in git...)
+push origin bash.exe: warning: could not find /tmp, please create!
+To C:/Documents and Settings/Silvia/.t\repo
+   83c6a5a..e1a1678  git-annex -> synced/git-annex
+   978ac14..e3e39fc  annex/direct/master -> synced/master
+
+ok
+commit  
+ok
+pull r2 bash.exe: warning: could not find /tmp, please create!
+From ../../.t\tmprepo35
+ * [new branch]      annex/direct/master -> r2/annex/direct/master
+ * [new branch]      git-annex  -> r2/git-annex
+ * [new branch]      master     -> r2/master
+ * [new branch]      synced/master -> r2/synced/master
+Updating 978ac14..e3e39fc
+Fast-forward
+ conflictor         | 1 -
+ conflictor/subfile | 1 +
+ 2 files changed, 1 insertion(+), 1 deletion(-)
+ delete mode 120000 conflictor
+ create mode 120000 conflictor/subfile
+Already up-to-date.
+
+
+
+ok
+(merging r2/git-annex into git-annex...)
+FAIL
+"""]]
diff --git a/doc/bugs/tmp_file_handling/comment_2_cc14c7a79a544e47654e4cd8abc85edd._comment b/doc/bugs/tmp_file_handling/comment_2_cc14c7a79a544e47654e4cd8abc85edd._comment
index e8e48abc8..d6ae5bcf0 100644
--- a/doc/bugs/tmp_file_handling/comment_2_cc14c7a79a544e47654e4cd8abc85edd._comment
+++ b/doc/bugs/tmp_file_handling/comment_2_cc14c7a79a544e47654e4cd8abc85edd._comment
@@ -4,5 +4,5 @@
  subject="comment 2"
  date="2012-10-24T15:50:40Z"
  content="""
-`rsynctmp` is only used when sending files to a rsync special remote. You can certianly delete it if you got a stale one, but the next time a file is sent to a rsync special remote it should delete it anyway.
+`rsynctmp` is only used when sending files to a rsync special remote. You can certainly delete it if you got a stale one, but the next time a file is sent to a rsync special remote it should delete it anyway.
 """]]
diff --git a/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build.mdwn b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build.mdwn
new file mode 100644
index 000000000..8f5e8c324
--- /dev/null
+++ b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build.mdwn
@@ -0,0 +1,11 @@
+As told in http://git-annex.branchable.com/bugs/OSX_app_issues/#comment-2a69d531bd3bb593c1a49dc8cdb34b1e the Mac OS 10.7.5 (Lion) build fails to run.
+
+    $ /Applications/git-annex.app/Contents/MacOS/git-annex
+
+    /Applications/git-annex.app/Contents/MacOS/runshell: line 25: syntax error near unexpected token `&'
+
+Manually editing /Applications/git-annex.app/Contents/MacOS/runshell as told in http://git-annex.branchable.com/bugs/OSX_app_issues/#comment-5579c2150ad4d2ccc207a253fe57612a fixes the issue.
+
+Furthermore, this build is quite outdated...
+
+> [[fixed|done]] --[[Joey]] 
diff --git a/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_1_e8df4b36a89b37edd94f3a318ae93a32._comment b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_1_e8df4b36a89b37edd94f3a318ae93a32._comment
new file mode 100644
index 000000000..d67330a22
--- /dev/null
+++ b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_1_e8df4b36a89b37edd94f3a318ae93a32._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-14T15:26:01Z"
+ content="""
+This is unfortunate.. The Lion autobuilder is running, but has been failing for various reasons for some time, and I have not managed to get ahold of Jimmy to fix them. Also, that machine may be upgraded from Lion before too long.
+"""]]
diff --git a/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_2_3b2c3c84bd1910280c549a2ee1c622b9._comment b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_2_3b2c3c84bd1910280c549a2ee1c622b9._comment
new file mode 100644
index 000000000..bd1763ca0
--- /dev/null
+++ b/doc/bugs/typo_on_the_Mac_OS_10.7.5_Lion_build/comment_2_3b2c3c84bd1910280c549a2ee1c622b9._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkSq2FDpK2n66QRUxtqqdbyDuwgbQmUWus"
+ nickname="Jimmy"
+ subject="comment 2"
+ date="2013-11-15T20:57:27Z"
+ content="""
+The builder is back, I was away from the office when it broke. It should be spitting out builds on a daily basis again.
+"""]]
diff --git a/doc/bugs/unfinished_repository_when_using_annex-ignore_true_.mdwn b/doc/bugs/unfinished_repository_when_using_annex-ignore_true_.mdwn
new file mode 100644
index 000000000..848f1b30b
--- /dev/null
+++ b/doc/bugs/unfinished_repository_when_using_annex-ignore_true_.mdwn
@@ -0,0 +1,25 @@
+### Please describe the problem.
+
+When using a git remote which doesn't support git-annex (f.e. gitlab) and is configured with `annex-ignore true` the remote is shown as `unfinished repository` in the webapp.
+
+It would be nice if the webapp would recognize this and show the remote as git-only remote including sync-state and remote name (or even better: the remote details, like the URL to the remote)
+
+### What steps will reproduce the problem?
+
+Add a normal git remote and configure `git config remote.<name>.annex-ignore true`.
+Start the webapp.
+
+### What version of git-annex are you using? On what operating system?
+
+    git-annex version: 4.20131101-gf59a6d1
+    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP Feeds Quvi TDFA
+    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
+    remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+    local repository version: 3
+    default repository version: 3
+    supported repository versions: 3 4
+    upgrade supported from repository versions: 0 1 2
+
+Kubuntu 13.10 x86_64
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/utf8/comment_13_7044d2c5bb1c91ee37eb9868963a1ff2._comment b/doc/bugs/utf8/comment_13_7044d2c5bb1c91ee37eb9868963a1ff2._comment
index fce51ac32..651e43438 100644
--- a/doc/bugs/utf8/comment_13_7044d2c5bb1c91ee37eb9868963a1ff2._comment
+++ b/doc/bugs/utf8/comment_13_7044d2c5bb1c91ee37eb9868963a1ff2._comment
@@ -37,5 +37,5 @@ And still cannot replicate the bug; as expected it does not use the socket since
 
 copy foo (checking foo...) [2013-07-27 16:40:42 EDT] call: ssh [\"-T\",\"fozz@git-annex-markdown.lang.speechmarks.com-fozz_phone.2Dannex.IdWwlXHtSsjVUMcq\",\"git-annex-shell 'inannex' '' 'SHA256E-s29--093429efb0d1427753d1f038f5279ec4df66785a1b2429b3fa5e3a01bcb75bd8' --uuid 111\"]
 
-So, I don't understand how this could have happened. Although my recent changes mean it'll use a 62 byte path max on Android now, which certianly should avoid the problem, even if there's some actual bug here that I cannot reproduce.
+So, I don't understand how this could have happened. Although my recent changes mean it'll use a 62 byte path max on Android now, which certainly should avoid the problem, even if there's some actual bug here that I cannot reproduce.
 """]]
diff --git a/doc/bugs/web_app_loops_over_a_non-addable_file.mdwn b/doc/bugs/web_app_loops_over_a_non-addable_file.mdwn
new file mode 100644
index 000000000..a1f490061
--- /dev/null
+++ b/doc/bugs/web_app_loops_over_a_non-addable_file.mdwn
@@ -0,0 +1,56 @@
+### Please describe the problem.
+
+I started the webapp on a pre-existing repo today, and it started adding all sorts of files which I didn't manually add, which is a little bit surprising, but "okay".
+
+The problem is that it would loop over this one file over and over again. Adding it on the commandline yields a proper error, but this doesn't seem to properly propagate to the frontend.
+
+### What steps will reproduce the problem?
+
+Unclear.
+
+### What version of git-annex are you using? On what operating system?
+
+4.20131105-g8efdc1a
+
+### Please provide any additional information below.
+
+Here's the daemon.log:
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+
+add clips/A31-05-12_21.22.amr (checksum...) [2013-11-06 10:21:10 EST] Committer: Committing changes to git
+[2013-11-06 10:21:11 EST] Committer: Adding A31-05-12_21.22.amr
+(Recording state in git...)
+(Recording state in git...)
+add clips/A31-05-12_21.22.amr (checksum...) [2013-11-06 10:21:11 EST] Committer: Committing changes to git
+[2013-11-06 10:21:12 EST] Committer: Adding A31-05-12_21.22.amr
+(Recording state in git...)
+(Recording state in git...)
+add clips/A31-05-12_21.22.amr (checksum...) [2013-11-06 10:21:12 EST] Committer: Committing changes to git
+[2013-11-06 10:21:13 EST] Committer: Adding A31-05-12_21.22.amr
+(Recording state in git...)
+add clips/A31-05-12_21.22.amr (checksum...) [2013-11-06 10:21:13 EST] Committer: Committing changes to git
+[2013-11-06 10:21:14 EST] Committer: Adding A31-05-12_21.22.amr
+(Recording state in git...)
+(Recording state in git...)
+add clips/A31-05-12_21.22.amr (checksum...) [2013-11-06 10:21:14 EST] Committer: Committing changes to git
+# End of transcript or log.
+"""]]
+
+And here's the attempt on the commandline, which is way more informative:
+
+[[!format sh """
+anarcat@marcos:video$ git annex add .
+add clips/96_257.mp3 ok
+add clips/A31-05-12_21.22.amr (checksum...)
+git-annex: /srv/video/.git/annex/objects/z3/96/SHA256E-s260070--46f0d657cdd79032d431e2aebb04b63685ab26e7d00963036e0b64c9f86998f8.22.amr/SHA256E-s260070--46f0d657cdd79032d431e2aebb04b63685ab26e7d00963036e0b64c9f86998f8.22.amr: setFileMode: permission denied (Operation not permitted)
+failed
+"""]]
+
+Turns out that file is owned by root, so it's an expected failure. But the webapp should simply skip this file, not loop over it.
+
+The workaround is obviously to give this file to the proper user. --[[anarcat]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/webapp_usability:_fails_mysteriously_on_newer_repo_layouts.mdwn b/doc/bugs/webapp_usability:_fails_mysteriously_on_newer_repo_layouts.mdwn
new file mode 100644
index 000000000..73908f40b
--- /dev/null
+++ b/doc/bugs/webapp_usability:_fails_mysteriously_on_newer_repo_layouts.mdwn
@@ -0,0 +1,34 @@
+### Please describe the problem.
+
+Starting the webapp on a repository that was hastily created by copying an existing one with an older version yields an undecipherable error.
+
+Rather minor.
+
+### What steps will reproduce the problem?
+
+1. Install git-annex from git
+2. make a repo
+3. copy it over to an external hard drive
+4. connect that drive to a wheezy box running git-annex from backports
+5. add the external hard drive to the webapp as a new repo
+6. boom
+
+I expected git-annex to tell me:
+
+    git-annex: Repository version 5 is not supported. Upgrade git-annex.
+
+Instead, it popped a red box saying a scary "Internal server error". I couldn't read the daemon logs either.
+
+### What version of git-annex are you using? On what operating system?
+
+original version is:
+
+    git-annex version: 5.20131109-gf2cb5b9
+
+the failing version is running the one from wheezy backports.
+
+### Please provide any additional information below.
+
+screenshot coming up.
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/builds.mdwn b/doc/builds.mdwn
index b6ada2bc2..49dfc8859 100644
--- a/doc/builds.mdwn
+++ b/doc/builds.mdwn
@@ -9,8 +9,8 @@
 <h2>Android</h2>
 <iframe width=1024 scrolling=no frameborder=0 marginheight=0 marginwidth=0 src="https://downloads.kitenet.net/git-annex/autobuild/android/">
 </iframe>
-<h2>OSX Mountain Lion</h2>
-<iframe width=1024 scrolling=no frameborder=0 marginheight=0 marginwidth=0 src="https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mountain-lion/">
+<h2>OSX Mavericks</h2>
+<iframe width=1024 scrolling=no frameborder=0 marginheight=0 marginwidth=0 src="https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mavericks/">
 </iframe>
 <h2>OSX Lion</h2>
 <iframe width=1024 scrolling=no frameborder=0 marginheight=0 marginwidth=0 src="http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/">
diff --git a/doc/design/assistant/blog/day_114__xmpp/comment_2_d14375dfb5791615802dab3c5438f8e2._comment b/doc/design/assistant/blog/day_114__xmpp/comment_2_d14375dfb5791615802dab3c5438f8e2._comment
index a18fa95e3..716f7d99a 100644
--- a/doc/design/assistant/blog/day_114__xmpp/comment_2_d14375dfb5791615802dab3c5438f8e2._comment
+++ b/doc/design/assistant/blog/day_114__xmpp/comment_2_d14375dfb5791615802dab3c5438f8e2._comment
@@ -4,5 +4,5 @@
  subject="comment 2"
  date="2012-11-09T21:55:42Z"
  content="""
-It does try to mark itself as extended away, but yes, I think this is a potential concern. If you find the assistant interacts badly with your other clients, you can certianly give it its own XMPP account.
+It does try to mark itself as extended away, but yes, I think this is a potential concern. If you find the assistant interacts badly with your other clients, you can certainly give it its own XMPP account.
 """]]
diff --git a/doc/design/assistant/blog/day_140__release_monday.mdwn b/doc/design/assistant/blog/day_140__release_monday.mdwn
index 5d732aef1..9c9ccd166 100644
--- a/doc/design/assistant/blog/day_140__release_monday.mdwn
+++ b/doc/design/assistant/blog/day_140__release_monday.mdwn
@@ -19,7 +19,7 @@ Still working on getting the standalone builds for this release done,
 should be done by the end of today.
 
 Also found a real stinker of a bug in `dirContentsRecursive`, which was
-just completely broken, apparently since day 1. Fixing that has certianly
+just completely broken, apparently since day 1. Fixing that has certainly
 fixed buggy behavior of `git annex import`. It seems that the other
 user of it, the transfer log code, luckily avoided the deep directory
 trees that triggered the bug.
diff --git a/doc/design/assistant/blog/day_76__pairing/comment_2_8e1b2233579bc26bfd758bbf6b3bdc07._comment b/doc/design/assistant/blog/day_76__pairing/comment_2_8e1b2233579bc26bfd758bbf6b3bdc07._comment
index 1ebc78627..a2e64671f 100644
--- a/doc/design/assistant/blog/day_76__pairing/comment_2_8e1b2233579bc26bfd758bbf6b3bdc07._comment
+++ b/doc/design/assistant/blog/day_76__pairing/comment_2_8e1b2233579bc26bfd758bbf6b3bdc07._comment
@@ -6,5 +6,5 @@
  content="""
 The [[bugs]] page is the place to put bug reports like this so I won't forget them.
 
-This should certianly not be happening. There are actually two git-annex processes running in the situation you describe; I'd be most curious to know whether the `git annex transfer` process was the one that blew up, or if the `git annex assistant` blew up. Also, it's not clear to me if you enabled the chunksize parameter when setting up the special remote, which could well be a significant detail.
+This should certainly not be happening. There are actually two git-annex processes running in the situation you describe; I'd be most curious to know whether the `git annex transfer` process was the one that blew up, or if the `git annex assistant` blew up. Also, it's not clear to me if you enabled the chunksize parameter when setting up the special remote, which could well be a significant detail.
 """]]
diff --git a/doc/design/assistant/blog/day_83__3-way.mdwn b/doc/design/assistant/blog/day_83__3-way.mdwn
index d58ec9fe5..9411c4c1c 100644
--- a/doc/design/assistant/blog/day_83__3-way.mdwn
+++ b/doc/design/assistant/blog/day_83__3-way.mdwn
@@ -68,6 +68,6 @@ still possible with other network topologies (ie, if D is connected to both
 B and C, there would be an upload loop 'B -> C -> D -> B`). So unless I can
 find a better event to hook into, this idea is doomed.
 
-I do have another idea to fix the same problem. C could certianly remember
+I do have another idea to fix the same problem. C could certainly remember
 that it saw a file and didn't know where to get the content from, and then
 when it receives a git push of a git-annex branch, try again.
diff --git a/doc/design/assistant/encrypted_git_remotes.mdwn b/doc/design/assistant/encrypted_git_remotes.mdwn
index 915f64d28..7d210a292 100644
--- a/doc/design/assistant/encrypted_git_remotes.mdwn
+++ b/doc/design/assistant/encrypted_git_remotes.mdwn
@@ -1,5 +1,5 @@
 Encrypted git remotes are now possible 
-using [git-remote-gcrypt](https://github.com/blake2-ppc/git-remote-gcrypt).
+using [git-remote-gcrypt](https://github.com/joeyh/git-remote-gcrypt).
 
 There are at least two use cases for this in the assistant:
 
diff --git a/doc/design/assistant/gpgkeys.mdwn b/doc/design/assistant/gpgkeys.mdwn
index e3f2a3a93..647d65083 100644
--- a/doc/design/assistant/gpgkeys.mdwn
+++ b/doc/design/assistant/gpgkeys.mdwn
@@ -7,7 +7,7 @@ To support using gpg keys in the assistant, we need some things:
 1. Help user set up a gpg key if they don't have one. This could be a
    special-purpose key dedicated to being used by git-annex. It might be
    nice to leave the user with a securely set up general purpose key,
-   but that would certianly preclude prompting for its password in the
+   but that would certainly preclude prompting for its password in the
    webapp. Indeed, the password prompt is the main problem here.
    Best solution would be to get gpg agent working on all supported 
    platforms.
diff --git a/doc/design/assistant/polls/2013_user_survey.mdwn b/doc/design/assistant/polls/2013_user_survey.mdwn
new file mode 100644
index 000000000..d1bac0ef8
--- /dev/null
+++ b/doc/design/assistant/polls/2013_user_survey.mdwn
@@ -0,0 +1 @@
+The 2013 git-annex user survey is in progress [[here|/polls/2013]].
diff --git a/doc/design/assistant/polls/Android_default_directory.mdwn b/doc/design/assistant/polls/Android_default_directory.mdwn
index 067a05c82..5b18e36df 100644
--- a/doc/design/assistant/polls/Android_default_directory.mdwn
+++ b/doc/design/assistant/polls/Android_default_directory.mdwn
@@ -4,4 +4,4 @@ Same as the desktop webapp, users will be able to enter a directory they
 want the first time they run it, but to save typing on android, anything
 that gets enough votes will be included in a list of choices as well.
 
-[[!poll open=yes expandable=yes 61 "/sdcard/annex" 6 "Whole /sdcard" 4 "DCIM directory (photos and videos only)" 1 "Same as for regular git-annex. ~/annex/"]]
+[[!poll open=yes expandable=yes 62 "/sdcard/annex" 6 "Whole /sdcard" 5 "DCIM directory (photos and videos only)" 1 "Same as for regular git-annex. ~/annex/"]]
diff --git a/doc/design/assistant/upgrading.mdwn b/doc/design/assistant/upgrading.mdwn
new file mode 100644
index 000000000..b1d658c8b
--- /dev/null
+++ b/doc/design/assistant/upgrading.mdwn
@@ -0,0 +1,52 @@
+The assistant should support upgrading itself.
+
+## non-distro upgrades
+
+When git-annex was installed from this website, the assistant should poll
+periodically (once a day or so) to see if there is a new version.
+It downloads, over https, a .info file, which contains a serialized data
+type containing upgrade information. The url it's downloaded from is
+configured by setting `UPGRADE_LOCATION` when building git-annex on the
+autobuilders.
+
+When a new version is found, the webapp prompts the user to start the
+upgrade. (annex.autoupgrade can be set to true to upgrade w/o prompting.)
+
+The upgrade process is automatic, and rather tricky. The file is downloaded
+using git-annex (as a regular key!), and is then unpacked into a new
+directory, and the programfile updated to point to it. Then git-annex
+restarts itself.
+
+### manifest files
+
+To clean up the old installation, a git-annex.MANIFEST file is looked for
+in it, and the files listed, as well as empty directories, are deleted.
+I don't want to accidentially delete something I didn't ship!
+
+## restart on upgrade
+
+When git-annex is installed from a proper distribution package, there is no
+need for the above. But, the assistant still needs to notice when git-annex
+get upgraded, and offer to restart (or automatically restart when
+annex.autoupgrade is set).
+
+This is done using the DirWatcher, watching the directory containing the
+git-annex binary. Or, in the case of a non-distro install, watching the
+directory where eg git-annex.linux/ was unpacked.
+
+When an change is detected, restart.
+
+## multi-daemon upgrades
+
+A single system may have multiple assistant daemons running in different
+repositories.
+
+In this case, one daemon should do the non-distro upgrade, and the rest
+should notice the upgrade and restart.
+
+I don't want every daemon trying to download the file at once..
+
+Approach: The first new version is installed into a stable directory, based
+on its version. So, start the upgrade by making this directory. If upgrade
+is already in progress, the directory will already exist. (Remove directory
+if upgrade fails.)
diff --git a/doc/design/roadmap.mdwn b/doc/design/roadmap.mdwn
index a35c661f1..34ddf0ed5 100644
--- a/doc/design/roadmap.mdwn
+++ b/doc/design/roadmap.mdwn
@@ -5,8 +5,8 @@ Now in the
 (starting September 2013).
 
 * Month 1 [[!traillink assistant/encrypted_git_remotes]]
-* **Month 2 [[!traillink assistant/disaster_recovery]]**
-* Month 3 user-driven features and polishing
+* Month 2 [[!traillink assistant/disaster_recovery]]
+* **Month 3 user-driven features and polishing** [[todo/direct_mode_guard]] [[assistant/upgrading]]
 * Month 4 improve special remote interface & git-annex enhancement contest
 * Month 5 [[!traillink assistant/xmpp_security]]
 * Month 6 Windows assistant and webapp
diff --git a/doc/devblog/day_-4__forgetting.mdwn b/doc/devblog/day_-4__forgetting.mdwn
index 9cec51475..a37b32e33 100644
--- a/doc/devblog/day_-4__forgetting.mdwn
+++ b/doc/devblog/day_-4__forgetting.mdwn
@@ -72,7 +72,7 @@ feature.
   to handle this case, too..
 
 * For some reason the automatic transitioning code triggers
-  a "(recovery from race)" commit. This is certianly a bug somewhere,
+  a "(recovery from race)" commit. This is certainly a bug somewhere,
   because you can't have a race with only 1 participant.
 
 ----
diff --git a/doc/devblog/day_47__fell_off_the_blogging_wagon.mdwn b/doc/devblog/day_47__fell_off_the_blogging_wagon.mdwn
new file mode 100644
index 000000000..fd312a0d8
--- /dev/null
+++ b/doc/devblog/day_47__fell_off_the_blogging_wagon.mdwn
@@ -0,0 +1,3 @@
+Low activity the past couple of days. Released a new version of git-annex
+yesterday. Today fixed three bugs (including a local pairing one that was
+pretty compicated) and worked on getting caught up with traffic.
diff --git a/doc/devblog/day_48__direct_mode_guard_design.mdwn b/doc/devblog/day_48__direct_mode_guard_design.mdwn
new file mode 100644
index 000000000..c047e7f75
--- /dev/null
+++ b/doc/devblog/day_48__direct_mode_guard_design.mdwn
@@ -0,0 +1,29 @@
+I've been investigating ways to implement a [[/todo/direct_mode_guard]].
+Preventing a stray `git commit -a` or `git add` doing bad things in a
+direct mode repository seems increasingly important.
+
+First, considered moving `.git`, so git won't know it's a git repository.
+This doesn't seem *too* hard to do, but there will certainly be unexpected
+places that assume `.git` is the directory name.
+
+I dislike it more and more as I think about it though, because it moves
+direct mode git-annex toward being entirely separate from git, and I don't
+want to write my own version control system. Nor do I want to complicate
+the git ecosystem with tools needing to know about git-annex to work in
+such a repository.
+
+So, I'm happy that one of the other ideas I tried today seems quite
+promising. Just set core.bare=true in a direct mode repository. This nicely
+blocks all git commands that operate on the working tree from doing
+anything, which is just what's needed in direct mode, since they don't know
+how to handle the direct mode files. But it lets all git commands and other
+tools that don't touch the working tree continue to be used. You can even
+run `git log file` in such a repository (surprisingly!)
+
+It also gives an easy out for anyone who really wants to use git commands
+that operate on the work tree of their direct mode repository, by just
+passing `-c core.bare=false`. And it's really easy to implement in
+git-annex too -- it can just notice if a repo has core.bare and
+annex.direct both set, and pass that parameter to every git command it
+runs. I should be able to get by with only modifying 2 functions to
+implement this.
diff --git a/doc/devblog/day_48__direct_mode_guard_design/comment_1_ec0147ccc55bad3a38652383f4098a65._comment b/doc/devblog/day_48__direct_mode_guard_design/comment_1_ec0147ccc55bad3a38652383f4098a65._comment
new file mode 100644
index 000000000..3f297d505
--- /dev/null
+++ b/doc/devblog/day_48__direct_mode_guard_design/comment_1_ec0147ccc55bad3a38652383f4098a65._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://id.koumbit.net/anarcat"
+ ip="70.82.37.38"
+ subject="awesome!"
+ date="2013-11-05T15:50:15Z"
+ content="""
+`core.bare=true` seems like an awesome idea!!! it probably means this can be factored into current installs without any change too right?
+"""]]
diff --git a/doc/devblog/day_49__direct_mode_guard_implementation.mdwn b/doc/devblog/day_49__direct_mode_guard_implementation.mdwn
new file mode 100644
index 000000000..ebc0dd494
--- /dev/null
+++ b/doc/devblog/day_49__direct_mode_guard_implementation.mdwn
@@ -0,0 +1,14 @@
+Long, long day coding up the direct mode guard today. About 90% of the fun
+is dealing with `receive.denyCurrentBranch` not preventing pushes that
+change the current branch, now that core.bare is set in direct mode.
+My current solution to this involves using a special branch when using
+direct mode, which nothing will ever push to (hopefully). A much nicer
+solution would be to use a `update` hook to deny pushes of the current
+branch -- but there are filesystems where repos cannot have git hooks.
+
+The test suite is falling over, but the `directguard` branch otherwise
+seems usable.
+
+----
+
+Today's work was sponsored by Carlo Matteo Capocasa.
diff --git a/doc/devblog/day_49__direct_mode_guard_implementation/comment_1_3ebe5c3f708070f164ecaf36b79f7bfc._comment b/doc/devblog/day_49__direct_mode_guard_implementation/comment_1_3ebe5c3f708070f164ecaf36b79f7bfc._comment
new file mode 100644
index 000000000..2a77d6d81
--- /dev/null
+++ b/doc/devblog/day_49__direct_mode_guard_implementation/comment_1_3ebe5c3f708070f164ecaf36b79f7bfc._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
+ nickname="Carlo"
+ subject="comment 1"
+ date="2013-11-06T11:50:00Z"
+ content="""
+Thanks, Joey! I am very proud!
+"""]]
diff --git a/doc/devblog/day_50__grab_bag.mdwn b/doc/devblog/day_50__grab_bag.mdwn
new file mode 100644
index 000000000..e38ec065c
--- /dev/null
+++ b/doc/devblog/day_50__grab_bag.mdwn
@@ -0,0 +1,34 @@
+Started by tracking down a strange bug that was apparently
+ubuntu-specific and caused git-annex branch changes to get committed to
+master. Root cause turned out to failing to recover from an
+exception. I'm kicking myself about that, because I remember looking at the
+code where the bug was at least twice before and thinking "hmm, should add
+exception handling here? nah..". Exceptions are horrible.
+
+Made a release with a fix for that and a few minor other accumulated
+changes since last Friday's release. The pain point of this release is to
+fix building without the webapp (so it will propigate to Debian testing,
+etc). This release does not include the direct mode guard, so I'll have a
+few weeks until the next release to get that tested.
+
+Fixed the test suite in `directguard`. This branch is now nearly ready to
+merge to master, but one command that is badly needed in guarded direct
+mode is "git status". So I am planning to rename "git annex status" to
+"git annex info", and make "git annex status" display something similar
+to "git status".
+
+Also took half an hour and added optional [[EKG]] support to git-annex.
+This is a Haskell library that can add a terrific monitoring console web
+UI to any program in 2 lines of code. Here we can see the git-annex
+webapp using resources at startup, followed in a few seconds by the
+assistant's startup scan of the repository.
+
+[[!img ekg/ekg.png]]
+
+BTW, Kevin tells me that the machine used to build git-annex for OSX is
+going to be upgraded to 10.9 soon. So, hopefully I'll be making autobuilds
+of that. I may have to stop the 10.8.2 autobuilds though.
+
+----
+
+Today's work was sponsored by [Protonet](http://protonet.info/).
diff --git a/doc/devblog/day_50__grab_bag/comment_1_01846f6494fe843889391fd09fd127a0._comment b/doc/devblog/day_50__grab_bag/comment_1_01846f6494fe843889391fd09fd127a0._comment
new file mode 100644
index 000000000..1c1717180
--- /dev/null
+++ b/doc/devblog/day_50__grab_bag/comment_1_01846f6494fe843889391fd09fd127a0._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://me.yahoo.com/a/2grhJvAC049fJnvALDXek.6MRZMTlg--#eec89"
+ nickname="John"
+ subject="OS X builds"
+ date="2013-11-07T05:12:13Z"
+ content="""
+Joey, were you not interested in my offer of an OS X build server that I've posted elsewhere on this list, and also in e-mail to you?
+"""]]
diff --git a/doc/devblog/day_50__grab_bag/comment_2_12736014aa2c1af81e4b83072505e7d5._comment b/doc/devblog/day_50__grab_bag/comment_2_12736014aa2c1af81e4b83072505e7d5._comment
new file mode 100644
index 000000000..70d7b7cd1
--- /dev/null
+++ b/doc/devblog/day_50__grab_bag/comment_2_12736014aa2c1af81e4b83072505e7d5._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 2"
+ date="2013-11-07T16:01:00Z"
+ content="""
+John, must have missed that; can't see to find it anywhere..
+"""]]
diff --git a/doc/devblog/day_51__direct_mode_guard_finished.mdwn b/doc/devblog/day_51__direct_mode_guard_finished.mdwn
new file mode 100644
index 000000000..9c637aa94
--- /dev/null
+++ b/doc/devblog/day_51__direct_mode_guard_finished.mdwn
@@ -0,0 +1,6 @@
+Finished the direct mode guard, including the new `git annex status`
+command.
+
+Spent the rest of the day working on various bug fixes. One of them turned
+into rather a lot of work to make the webapp's UI better for git
+remotes that do not have an annex.uuid.
diff --git a/doc/devblog/day_52__slowly_but_surely.mdwn b/doc/devblog/day_52__slowly_but_surely.mdwn
new file mode 100644
index 000000000..01019355b
--- /dev/null
+++ b/doc/devblog/day_52__slowly_but_surely.mdwn
@@ -0,0 +1,5 @@
+Been chipping away at my backlog of messages, and it's down to 23 items.
+
+Finally managed to get ghc to build with a newer version of the NDK.
+This *might* mean a solution to git-annex on Android 4.2. I 
+[need help with testing](http://git-annex.branchable.com/bugs/git-annex_broken_on_Android_4.3/#comment-90b82735cd6090a7765f423b743fffd3).
diff --git a/doc/devblog/day_54__android_bisection_minions.mdwn b/doc/devblog/day_54__android_bisection_minions.mdwn
new file mode 100644
index 000000000..ed86c68d0
--- /dev/null
+++ b/doc/devblog/day_54__android_bisection_minions.mdwn
@@ -0,0 +1,9 @@
+Finally found the [root cause](http://git-annex.branchable.com/bugs/git-annex_broken_on_Android_4.3/#comment-452bee7d0a816300ccb4a34f9758134e)
+of the Android 4.3/4.4 trouble, and a fix is now in place!
+
+As a bonus, it looks like I've fixed a problem accessing the
+environment on Android that had been worked around in an ugly way before.
+
+Big thanks to my remote hands Michael Alan, Sören, and subito. All
+told they ran 19 separate tests to help me narrow down this tricky
+problem, often repeating long command lines on software keyboards.
diff --git a/doc/devblog/day_54__android_bisection_minions/comment_1_bea8fbe2b87d4a4865b92fa796298fa0._comment b/doc/devblog/day_54__android_bisection_minions/comment_1_bea8fbe2b87d4a4865b92fa796298fa0._comment
new file mode 100644
index 000000000..0f8e58827
--- /dev/null
+++ b/doc/devblog/day_54__android_bisection_minions/comment_1_bea8fbe2b87d4a4865b92fa796298fa0._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmW0kg4uiMIhSHeVuvJFyo2VYMl7Qoej0s"
+ nickname="Chris"
+ subject="Woot!"
+ date="2013-11-12T15:52:48Z"
+ content="""
+Thanks for getting this fixed.  I'm about to go on a long plane ride, and this will make it a lot easier for me to put movies on my tablet.
+"""]]
diff --git a/doc/devblog/day_55__fireside_porting.mdwn b/doc/devblog/day_55__fireside_porting.mdwn
new file mode 100644
index 000000000..c7469d953
--- /dev/null
+++ b/doc/devblog/day_55__fireside_porting.mdwn
@@ -0,0 +1,22 @@
+Annoyingly, the Android 4.3 fix breaks git-annex on Android 4.0 (probably
+through 4.2), so I now have two separate builds of the Android app.
+
+---
+
+Worked on Windows porting today. I've managed to get the assistant
+and watcher (but not yet webapp) to build on Windows.
+The `git annex transferrer` interface needs POSIX stuff, and seems to be
+the main thing that will need porting for Windows for the assistant to
+work, besides of course file change detection. For that, I've hooked up
+[Win32-notify](http://hackage.haskell.org/package/Win32-notify).
+
+So the watcher might work on Windows. 
+At least in theory. Problem is, while all the code builds ok, 
+it fails to link:
+
+	ghc.exe: could not execute: C:\Program Files (x86)\Haskell Platform\2012.4.0.0\lib/../mingw/bin/gcc.exe
+
+I wonder if this is case of too many parameters being passed?
+
+This happens both on the autobuilder and on my laptop, so I'm stuck here.
+Oh well, I was not planning to work on this anyway until February...
diff --git a/doc/devblog/day_55__fireside_porting/comment_1_d690a52db82f9594d99ae65fe51e1f1a._comment b/doc/devblog/day_55__fireside_porting/comment_1_d690a52db82f9594d99ae65fe51e1f1a._comment
new file mode 100644
index 000000000..74acc8322
--- /dev/null
+++ b/doc/devblog/day_55__fireside_porting/comment_1_d690a52db82f9594d99ae65fe51e1f1a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://nullroute.eu.org/~grawity/"
+ nickname="Mantas"
+ subject="comment 1"
+ date="2013-11-13T06:22:49Z"
+ content="""
+[ProcExp](http://technet.microsoft.com/en-us/sysinternals/bb896645.aspx) may be useful -- it can show process-related syscalls and their return codes _(among other things like file or registry access)_ so it should tell exactly why the exec failed.
+"""]]
diff --git a/doc/devblog/day_56__git-annex_user_survey.mdwn b/doc/devblog/day_56__git-annex_user_survey.mdwn
new file mode 100644
index 000000000..8c1c67994
--- /dev/null
+++ b/doc/devblog/day_56__git-annex_user_survey.mdwn
@@ -0,0 +1,20 @@
+One of my goals for this month is to get a better sense of how git-annex is
+being used, how it's working out for people, and what areas need to be
+concentrated on. To start on that, I am doing the 
+[2013 git-annex user survey](http://git-annex-survey.branchable.com/polls/2013/), similar to the git user
+surveys. I will be adding some less general polls later (suggestions for
+topics appreciated!), but you can go vote in any or all of 10 polls now.
+
+----
+
+Found a workaround for yesterday's Windows build problem. Seems that only
+cabal runs gcc in a way that fails, so `ghc --make` builds is successfully.
+However, the watcher doesn't quite work on Windows. It does get events when
+files are created, but it seems to then hang before it can add the file to
+git, or indeed finish printing out a debug log message about the event.
+This looks like it could be a problem with the threaded ghc runtime on
+Windows, or something like that.
+
+Main work today was improving the git repository repair to handle corrupt
+index files. The assistant can now start up, detect that the index file is
+corrupt, and regenerate it all automatically.
diff --git a/doc/devblog/day_57__mavericks.mdwn b/doc/devblog/day_57__mavericks.mdwn
new file mode 100644
index 000000000..1031895be
--- /dev/null
+++ b/doc/devblog/day_57__mavericks.mdwn
@@ -0,0 +1,14 @@
+The user survey is producing some interesting and useful results!  
+Added two more polls: [using with](http://git-annex-survey.branchable.com/polls/2013/using_with/) and [blocking problems](http://git-annex-survey.branchable.com/polls/2013/blocking_problems/)  
+(There were some load issues so if you were unable to vote yesterday, try
+again..)
+
+Worked on getting the autobuilder for OS X Mavericks set up. Eventually
+succeeded, after patching a few packages to work around a cpp that thinks
+it should parse haskell files as if they're C code.
+Also, Jimmy has resuscitated the OS X Lion autobuilder.
+
+A not too bad bug in automatic merge conflict resolution has been reported,
+so I will need to dig into that tomorrow. Didn't feel up to it today, so
+instead have been spending the remaining time finishing up a branch that
+switches the test suite to use the tasty test framework.
diff --git a/doc/devblog/day_58__urgle.mdwn b/doc/devblog/day_58__urgle.mdwn
new file mode 100644
index 000000000..f6d930d80
--- /dev/null
+++ b/doc/devblog/day_58__urgle.mdwn
@@ -0,0 +1,16 @@
+Fixed two difficult bugs with direct mode. One happened (sometimes) when a
+file was deleted and replaced with a directory by the same name and then
+those changes were merged into a direct mode repository.
+
+The other problem was that direct mode did not prevent writes to
+.git/annex/objects the way that indirect mode does, so when a file in the
+repository was not currently present, writing to the dangling symlink would
+follow it and write into the object directory.
+
+Hmm, I was going to say that it's a pity that direct mode still has so many
+bugs being found and fixed, but the last real bug fix to direct mode was
+made last May! Instead, I probably have to thank Tim for being a very
+thorough tester.
+
+Finished switching the test suite to use the tasty framework, and prepared
+tasty packages for Debian.
diff --git a/doc/devblog/day_58__urgle/comment_1_bd279f58f614b103a53215dfb0211007._comment b/doc/devblog/day_58__urgle/comment_1_bd279f58f614b103a53215dfb0211007._comment
new file mode 100644
index 000000000..0fec5fa8c
--- /dev/null
+++ b/doc/devblog/day_58__urgle/comment_1_bd279f58f614b103a53215dfb0211007._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkx5V3MTbzCXS3J7Mn9FEq8M9bPPYMkAHY"
+ nickname="Pedro"
+ subject="Is direct mode still using symlinks then?"
+ date="2013-11-16T16:28:39Z"
+ content="""
+Is direct mode still using symlinks? I see the bug I opened is still unclosed:
+
+http://git-annex.branchable.com/bugs/Direct_mode_repositories_still_use_symlinks_sometimes/
+
+Any opinion on this? This is still my main problem with replacing dropbox with git-annex.
+"""]]
diff --git a/doc/devblog/day_59__release_day.mdwn b/doc/devblog/day_59__release_day.mdwn
new file mode 100644
index 000000000..469ccec44
--- /dev/null
+++ b/doc/devblog/day_59__release_day.mdwn
@@ -0,0 +1,11 @@
+Release today, right on bi-weekly schedule. Rather startled
+at the size of the changelog for this one; along with the direct mode
+guard, it adds support for OS X Mavericks, Android 4.3/4.4, and fixes
+numerous bugs.
+
+Posted another question in the survey,
+<http://git-annex-survey.branchable.com/polls/2013/roadmap/>.
+
+Spun off git-repair as an independant package from git-annex. Of course,
+most of the source code is shared with git-annex. I need to do something
+with libraries eventually..
diff --git a/doc/devblog/day_60__damage_driven_development.mdwn b/doc/devblog/day_60__damage_driven_development.mdwn
new file mode 100644
index 000000000..64460e86a
--- /dev/null
+++ b/doc/devblog/day_60__damage_driven_development.mdwn
@@ -0,0 +1,36 @@
+Wrote some evil code you don't want to run today. Git.Destroyer randomly
+generates Damage, and applies it to a git repository, in a way that is
+reproducible -- applying the same Damage to clones of the same git repo 
+will always yeild the same result.
+
+This let me build a test harness for git-repair, which repeatedly clones,
+damages, and repairs a repository. And when it fails, I can just ask it to
+retry after fixing the bug and it'll re-run every attempt it's logged.
+
+This is already yeilding improvements to the git-repair code.
+The first randomly constructed Damage that it failed to recover
+turned out to be a truncated index file that hid some other
+corrupted object files from being repaired.
+
+	[Damage Empty (FileSelector 1),
+	 Damage Empty (FileSelector 2),
+	 Damage Empty (FileSelector 3),
+	 Damage Reverse (FileSelector 3),
+	 Damage (ScrambleFileMode 3) (FileSelector 5),
+	 Damage Delete (FileSelector 9),
+	 Damage (PrependGarbage "¥SOH¥STX¥ENQ¥f¥a¥ACK¥b¥DLE¥n") (FileSelector 9),
+	 Damage Empty (FileSelector 12),
+	 Damage (CorruptByte 11 25) (FileSelector 6),
+	 Damage Empty (FileSelector 5),
+	 Damage (ScrambleFileMode 4294967281) (FileSelector 14)
+	]
+
+I need to improve the ranges of files that it damages -- currently QuickCheck
+seems to only be selecting one of the first 20 or so files. Also, it's quite
+common that it will damage `.git/config` so badly that git thinks it's not
+a git repository anymore. I am not sure if that is something `git-repair`
+should try to deal with.
+
+---
+
+Today's work was sponsored by the WikiMedia Foundation.
diff --git a/doc/devblog/day_61__damage_driven_development__II.mdwn b/doc/devblog/day_61__damage_driven_development__II.mdwn
new file mode 100644
index 000000000..605a3878d
--- /dev/null
+++ b/doc/devblog/day_61__damage_driven_development__II.mdwn
@@ -0,0 +1,15 @@
+Pushed out a minor release of git-annex today, mostly to fix build problems
+on Debian. No strong reason to upgrade to it otherwise.
+
+Continued where I left off with the Git.Destroyer. Fixed quite a lot of
+edge cases where git repair failed due to things like a corrupted .git/HEAD
+file (this makes git think it's not in a git repository), corrupt
+git objects that have an unknown object type and so crash git hard, and
+an interesting failure mode where git fsck wants to allocate 116 GB of
+memory due to a corrupted object size header. Reported that last to the git
+list, as well as working around it.
+
+At the end of the day, I ran a test creating 10000 corrupt git
+repositories, and **all** of them were recovered! Any improvements will
+probably involve finding new ways to corrupt git repositories that my code
+can't think of. ;)
diff --git a/doc/devblog/day_62__upgrade_alerts.mdwn b/doc/devblog/day_62__upgrade_alerts.mdwn
new file mode 100644
index 000000000..0b3078563
--- /dev/null
+++ b/doc/devblog/day_62__upgrade_alerts.mdwn
@@ -0,0 +1,22 @@
+Still working on the git repair code. Improved the test suite, which found
+some more bugs, and so I've been running tests all day and occasionally
+going and fixing a bug in the repair code. The hardest part of repairing a
+git repo has turned out to be reliably determining which objects in it are
+broken. Bugs in git don't help (but the git devs are going to fix the one I
+reported).
+
+But the interesting new thing today is that I added some upgrade alert code
+to the webapp. Ideally everyone would get git-annex and other software as
+part of an OS distribution, which would include its own upgrade system -- 
+But the  [survey](http://git-annex-survey.branchable.com/polls/2013/how_installed/)
+tells me that a quarter of installs are from the prebuilt binaries I
+distribute.
+
+So, those builds are going to be built with knowledge of an upgrade url,
+and will periodically download a small info file (over https) to see if a
+newer version is available, and show an alert.
+
+I think all that's working, though I have not yet put the info files in
+place and tested it. The actual upgrade process will be a manual
+download and reinstall, to start with, and then perhaps I'll automate it
+further, depending on how hard that is on the different platforms.
diff --git a/doc/devblog/day_62__upgrade_alerts/comment_1_cdb44aaa1d2a784a72613cbf16038f89._comment b/doc/devblog/day_62__upgrade_alerts/comment_1_cdb44aaa1d2a784a72613cbf16038f89._comment
new file mode 100644
index 000000000..cb0bfc08b
--- /dev/null
+++ b/doc/devblog/day_62__upgrade_alerts/comment_1_cdb44aaa1d2a784a72613cbf16038f89._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawniayrgSdVLUc3c6bf93VbO-_HT4hzxmyo"
+ nickname="Tobias"
+ subject="gitannex-install"
+ date="2013-11-22T07:13:02Z"
+ content="""
+To install and upgrade the prebuilt binary on Linux I use the fantastic [gitannex-install](https://github.com/zerodogg/scriptbucket/blob/master/gitannex-install) script, together with the upgrade alert this is just great.
+"""]]
diff --git a/doc/devblog/day_62__upgrade_alerts/comment_2_b08bb946e4760d7f03b45c852c745b2e._comment b/doc/devblog/day_62__upgrade_alerts/comment_2_b08bb946e4760d7f03b45c852c745b2e._comment
new file mode 100644
index 000000000..3a5ec5b7d
--- /dev/null
+++ b/doc/devblog/day_62__upgrade_alerts/comment_2_b08bb946e4760d7f03b45c852c745b2e._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="git-annex release annex"
+ date="2013-11-25T06:15:23Z"
+ content="""
+Immediate thought: instead of an info file, why not sync a public git repo with releases annexed with URLs?
+"""]]
diff --git a/doc/devblog/day_63__leverage.mdwn b/doc/devblog/day_63__leverage.mdwn
new file mode 100644
index 000000000..6cf8acfa2
--- /dev/null
+++ b/doc/devblog/day_63__leverage.mdwn
@@ -0,0 +1,24 @@
+The difference picking the right type can make! Last night, I realized that
+the where I had a `distributionSha256sum :: String`, I should instead use
+`distributionKey :: Key`. This means that when git-annex is eventually
+downloading an upgrade, it can treat it as just another Key being
+downloaded from the web. So the webapp will show that transfer along with
+all the rest, and I can leverage tons of code for a new purpose. For
+example, it can simply fsck the key once it's downloaded to verify its
+checksum.
+
+Also, built a DistriutionUpdate program, which I'll run to generate the
+info files for a new version. And since I keep git-annex releases in a
+git-annex repo, this too leverages a lot of git-annex modules, and ended up
+being just 60 easy lines of code. The upgrade notification code is tested
+and working now.
+
+And, I made the assistant detect when the git-annex program binary is
+replaced or modified. Used my existing DirWatcher code for that. The plan
+is to restart the assistant on upgrade, although I need to add some sanity
+checks (eg, reuse the lsof code) first. And yes, this will work even for
+`apt-get upgrade`!
+
+----
+
+Today's work was sponsored by Paul Tötterman
diff --git a/doc/devblog/day_64__overkill.mdwn b/doc/devblog/day_64__overkill.mdwn
new file mode 100644
index 000000000..fd5d66f4e
--- /dev/null
+++ b/doc/devblog/day_64__overkill.mdwn
@@ -0,0 +1,31 @@
+Completely finished up with making the assistant detect when git-annex's
+binary has changed and handling the restart.
+
+It's a bit tricky because during an upgrade there can be two assistant
+daemons running at the same time, in the same repository. Although I
+disable the watcher of the old one first. Luckily, git-annex has long
+supported running multiple concurrent git-annex processes in the same
+repository.
+
+The surprisingly annoying part turned out to be how to make the webapp
+redirect the browser to the new url when it's upgraded. Particularly needed
+when automatic upgrades are enabled, since the user will not then be taking
+any action in the webapp that could result in a redirect. My solution to this
+feels like overkill; the webapp does ajax long polling until it gets an
+url, and then redirects to it. Had to write javascript code and ugh.
+
+But, that turned out to also be useful when manually restarting the webapp
+(removed some horrible old code that ran a shell script to do it before),
+and also when shutting the webapp down.
+
+[[!img assistant/downloadupgrade.png alt="assistant downloading an upgrade to itself"]]
+
+Getting back to upgrades, I have the assistant downloading the upgrade, and
+running a hook action once the key is transferred. Now all I need is some
+platform-specific code to install it. Will probably be hairy, especially on
+OSX where I need to somehow unmount the old git-annex dmg and mount the new
+one, from within a program running on the old dmg.
+
+----
+
+Today's work was sponsored by Evan Deaubl.
diff --git a/doc/devblog/day_64__overkill/comment_1_e1db7678aae37af281d31ae211677786._comment b/doc/devblog/day_64__overkill/comment_1_e1db7678aae37af281d31ae211677786._comment
new file mode 100644
index 000000000..b04af39ff
--- /dev/null
+++ b/doc/devblog/day_64__overkill/comment_1_e1db7678aae37af281d31ae211677786._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="abg"
+ ip="184.75.210.234"
+ subject="Upgrade installation in OSX"
+ date="2013-11-24T00:28:03Z"
+ content="""
+Hey,
+
+You don't have to implement any whacky DMG replacement logic for OSX upgrades. No sane user will be using the application from the DMG. They will drag the .app directory to /Applications or some non-standard location and unmount the DMG.  So your upgrade logic for OSX should end up looking very similar to the upgrade logic for Linux.
+"""]]
diff --git a/doc/devblog/day_64__overkill/comment_3_f7a96f0b6d942d0b59d9d0ec1b21c4bf._comment b/doc/devblog/day_64__overkill/comment_3_f7a96f0b6d942d0b59d9d0ec1b21c4bf._comment
new file mode 100644
index 000000000..c9e76b577
--- /dev/null
+++ b/doc/devblog/day_64__overkill/comment_3_f7a96f0b6d942d0b59d9d0ec1b21c4bf._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmuh_0-Mjz7QkVz7gT_7PRpCgmMcBFkj14"
+ nickname="Wichert"
+ subject="Running from DMG is not a sane use-case"
+ date="2013-11-25T08:23:38Z"
+ content="""
+I don't think you should bother trying to support upgrades when people are running from a dmg. A DMG is just a disk image, and a format commonly used to distribute software. Running software from a DMG is not something anyone does beyond a quick first test of an application. A more reasonable thing to do, which many applications do now, is to offer to move the application from the DMG to /Applications if you detect someone is running it from a DMG.
+"""]]
diff --git a/doc/devblog/day_65__wrapping_up_upgrades.mdwn b/doc/devblog/day_65__wrapping_up_upgrades.mdwn
new file mode 100644
index 000000000..9faa31a63
--- /dev/null
+++ b/doc/devblog/day_65__wrapping_up_upgrades.mdwn
@@ -0,0 +1,5 @@
+[[!img assistant/upgradecomplete.png]]
+
+Upgrades are fully working on Linux. OSX code is written but intested and I
+thought of one bug it certainly has on my evening walk. Probably another
+hour's work left later this evening to finish it off.
diff --git a/doc/devblog/day_66__upgrade_testing.mdwn b/doc/devblog/day_66__upgrade_testing.mdwn
new file mode 100644
index 000000000..741ec494e
--- /dev/null
+++ b/doc/devblog/day_66__upgrade_testing.mdwn
@@ -0,0 +1,17 @@
+Upgrades should be working on OSX Mavericks, Linux, and sort of on Android.
+This needs more testing, so I have temporarily made the daily builds think
+they are an older version than the last git-annex release. So when you
+install a daily build, and start the webapp, it should try to upgrade
+(really downgrade) to the last release. Tests appreciated.
+
+Looking over the whole upgrade code base, it took 700 lines of code
+to build the whole thing, of which 75 are platform specific (and mostly
+come down to just 3 or 4 shell commands). Not bad..
+
+----
+
+Last night, added support for quvi 0.9, which has a completely changed
+command line interface from the 0.4 version.
+
+Plan to spend tomorrow catching up on bug reports etc and then low activity
+for rest of the week.
diff --git a/doc/devblog/day_67_thanksgiving_rush.mdwn b/doc/devblog/day_67_thanksgiving_rush.mdwn
new file mode 100644
index 000000000..7ac6ba523
--- /dev/null
+++ b/doc/devblog/day_67_thanksgiving_rush.mdwn
@@ -0,0 +1,19 @@
+My last day before thanksgiving, getting caught up with some recent bug
+reports and, quite a rush to get a lot of fixes in. Adding to the fun,
+wintery weather means very limited power today.
+
+It was a very productive day, especially for Android, which hopefully has
+XMPP working again (at least it builds..), halved the size of the package,
+etc.
+
+Fixed a stupid bug in the automatic v5 upgrade code; annex.version was not
+being set to 5, and so every git annex command was
+actually re-running the upgrade.
+
+Fixed another bug I introduced last Friday, which the test suite luckily
+caught, that broke using some local remotes in direct mode.
+
+Tracked down a behavior that makes `git annex sync` quite slow on
+filesystems that don't support symlinks. I need to switch direct mode to 
+not using `git commit` at all, and use plumbing to make commits there.
+Will probably work on this over the holiday.
diff --git a/doc/devblog/day_9__Friday_the_13th.mdwn b/doc/devblog/day_9__Friday_the_13th.mdwn
index b8fe4bc19..77d9039eb 100644
--- a/doc/devblog/day_9__Friday_the_13th.mdwn
+++ b/doc/devblog/day_9__Friday_the_13th.mdwn
@@ -10,7 +10,7 @@ But, I got distracted chasing down some bugs on Windows. These were
 quite ugly; more direct mode mapping breakage which resulted in 
 files not being accessible. Also fsck on Windows failed to detect and fix
 the problem. All fixed now. (If you use git-annex on Windows, you should
-certianly upgrade and run `git annex fsck`.)
+certainly upgrade and run `git annex fsck`.)
 
 As with most bugs in the Windows port, the underlying cause turned out to
 be stupid: `isSymlink` always returned False on Windows. Which makes sense
diff --git a/doc/direct_mode.mdwn b/doc/direct_mode.mdwn
index a6a2003a7..749d3a6e2 100644
--- a/doc/direct_mode.mdwn
+++ b/doc/direct_mode.mdwn
@@ -4,8 +4,7 @@ git, and in turn point at the content of large files that is stored in
 
 The advantage of direct mode is that you can access files directly,
 including modifying them. The disadvantage is that most regular git
-commands cannot safely be used, and only a subset of git-annex commands
-can be used.
+commands cannot be used in a direct mode repository.
 
 Normally, git-annex repositories start off in indirect mode. With some
 exceptions:
@@ -21,7 +20,7 @@ exceptions:
 Any repository can be converted to use direct mode at any time, and if you
 decide not to use it, you can convert back to indirect mode just as easily.
 Also, you can have one clone of a repository using direct mode, and another
-using indirect mode; direct mode interoperates.
+using indirect mode.
 
 To start using direct mode:
 
@@ -52,7 +51,6 @@ computers, and manage your files, this should not be a concern for you.
 ## use a direct mode repository
 
 You can use most git-annex commands as usual in a direct mode repository.
-A very few commands don't work in direct mode, and will refuse to do anything.
 
 Direct mode also works well with the git-annex assistant.
 
@@ -63,23 +61,33 @@ the changes to other repositories for `git annex sync` there to pick up,
 and will pull and merge any changes made on other repositories into the
 local repository.
 
-While you generally will just use `git annex sync`, if you want to,
-you can use `git commit --staged`, or plain `git commit`.
-But not `git commit -a`, or `git commit <file>` ..
-that'd commit whole large files into git!
-
 ## what doesn't work in direct mode
 
-`git annex status` shows incomplete information. A few other commands,
-like `git annex unlock` don't make sense in direct mode and will refuse to
-run.
+A very few git-annex commands don't work in direct mode, and will refuse
+to do anything. For example, `git annex unlock` doesn't make sense in
+direct mode.
+
+As for git commands, direct mode prevents using any git command that would
+modify or access the work tree. So you cannot `git commit` or `git pull`
+(use `git annex sync` for both instead), or run `git status` (use `git
+annex status` instead). These git commands will complain "fatal: This
+operation must be run in a work tree".
+
+The reason for this is that git doesn't understand how git-annex uses the
+work tree in direct mode. Where git expects the symlinks that get checked
+into git to be checked out in the work tree, direct mode instead replaces
+them with the actual content of files, as managed by git-annex.
+
+There are still lots of git commands you can use in direct mode. For
+example, you can run `git log` on files, run `git push`, `git fetch`,
+`git config`, `git remote add` etc.
+
+## forcing git to use the work tree in direct mode
 
-As for git commands, you can probably use some git working tree
-manipulation commands, like `git checkout` and `git revert` in useful
-ways... But beware, these commands can replace files that are present in
-your repository with broken symlinks. If that file was the only copy you
-had of something, it'll be lost. 
+This is for experts only. You can lose data doing this, or check enormous
+files directly into your git repository, and it's your fault if you do!
+Also, there should be no good reason to need to do this, ever.
 
-This is one more reason it's wise to make git-annex untrust your direct mode
-repositories. Still, you can lose data using these sort of git commands, so
-use extreme caution.
+Ok, with the warnings out of the way, all you need to do to make any
+git command access the work tree in direct mode is pass it 
+`-c core.bare=false`
diff --git a/doc/direct_mode/comment_10_94284a476604e9c812b7ee475ca22959._comment b/doc/direct_mode/comment_10_94284a476604e9c812b7ee475ca22959._comment
deleted file mode 100644
index e14f56485..000000000
--- a/doc/direct_mode/comment_10_94284a476604e9c812b7ee475ca22959._comment
+++ /dev/null
@@ -1,12 +0,0 @@
-[[!comment format=mdwn
- username="http://olivier.berger.myopenid.com/"
- nickname="obergix"
- subject="How to sync changes made in another remote when in direct mode"
- date="2013-08-17T21:53:57Z"
- content="""
-Re-reading @joey's reponse above, I see that merge/pull don't seem to be safe and will create dangling symlinks. That corresponds to those files I can see on cifs, I guess.
-
-But then, how can a direct repo sync with changes made in other remotes, if there no pull/fetch available.
-
-Can it then be only the source of changes which will propagate to indirect remotes ?
-"""]]
diff --git a/doc/direct_mode/comment_1_93fc31e8dc0ad16248a2593a1482d375._comment b/doc/direct_mode/comment_1_93fc31e8dc0ad16248a2593a1482d375._comment
deleted file mode 100644
index 8de8cf9af..000000000
--- a/doc/direct_mode/comment_1_93fc31e8dc0ad16248a2593a1482d375._comment
+++ /dev/null
@@ -1,8 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawl2Jj8q2upJL4ZQAc2lp7ugTxJiGtcICv8"
- nickname="Michael"
- subject="comment 1"
- date="2013-02-18T23:24:11Z"
- content="""
-So, just which git commands *are* safe?  It seems like I'm going to have to use direct mode, so it'd be nice to know just what I'm allowed to do, and what the workflow should be.
-"""]]
diff --git a/doc/direct_mode/comment_2_7f7086b34ed136851963f145868a1d23._comment b/doc/direct_mode/comment_2_7f7086b34ed136851963f145868a1d23._comment
deleted file mode 100644
index ddabee7e3..000000000
--- a/doc/direct_mode/comment_2_7f7086b34ed136851963f145868a1d23._comment
+++ /dev/null
@@ -1,12 +0,0 @@
-[[!comment format=mdwn
- username="http://joeyh.name/"
- ip="4.152.108.183"
- subject="safe and unsafe commands"
- date="2013-02-19T02:55:13Z"
- content="""
-All git commands that do not change files in the work tee (and do not stage files from the work tree), are safe. I don't have a complete list; it includes `git log`, `git show`, `git diff`, `git commit` (but not -a or with a file as a parameter), `git branch`, `git fetch`, `git push`, `git grep`, `git status`, `git tag`, `git mv` (this one is somewhat surprising, but I've tested it and it's ok)
-
-git commands that change files in the work tree will replace your data with dangling symlinks. This includes things like `git revert`, `git checkout`, `git merge`, `git pull`, `git reset`
-
-git commands that stage files from the work tree will commit your data to git directly. This includes `git add`, `git commit -a`, and `git commit file`
-"""]]
diff --git a/doc/direct_mode/comment_4_97c26bd82f623a3b2d56bab4afff0126._comment b/doc/direct_mode/comment_4_97c26bd82f623a3b2d56bab4afff0126._comment
index 180018399..cf5ae2fb6 100644
--- a/doc/direct_mode/comment_4_97c26bd82f623a3b2d56bab4afff0126._comment
+++ b/doc/direct_mode/comment_4_97c26bd82f623a3b2d56bab4afff0126._comment
@@ -6,7 +6,6 @@
  content="""
 <pre>
 git annex add $file
-git commit -m changed
 git annex sync
 git annex copy $file --to otherrepo
 </pre>
diff --git a/doc/direct_mode/comment_9_cff56dbcdfec60375c30d5b1b1c60614._comment b/doc/direct_mode/comment_9_cff56dbcdfec60375c30d5b1b1c60614._comment
deleted file mode 100644
index d2c752a54..000000000
--- a/doc/direct_mode/comment_9_cff56dbcdfec60375c30d5b1b1c60614._comment
+++ /dev/null
@@ -1,12 +0,0 @@
-[[!comment format=mdwn
- username="http://olivier.berger.myopenid.com/"
- nickname="obergix"
- subject="Mixing indirect mode and direct mode on different remotes"
- date="2013-08-17T20:35:40Z"
- content="""
-I'd like to have an indirect mode repo on my laptop cloned on a cifs mount point (mounted off an SMB NAS) thus in direct mode. But all I can see on the clone after merge/pull is text files of length 207 chars containg the symlink in plain text.
-
-I guess this is what git manages internally for the symlinks... so I'm afraid git annex doesn't work in such case.
-
-Can you confirm that indirect and direct modes can coexist on clones of the same repo ?
-"""]]
diff --git a/doc/ekg.mdwn b/doc/ekg.mdwn
new file mode 100644
index 000000000..3bbea8614
--- /dev/null
+++ b/doc/ekg.mdwn
@@ -0,0 +1,14 @@
+You can `cabal configure -fEKG` to build a git-annex that includes
+the EKG remote monitoring interface.
+
+To access the EKG control panel, go to
+<http://localhost:4242/> while a git-annex command is running.
+
+This EKG build is mostly useful for debugging resource usage problems.
+
+[[!img ekg.png caption="git-annex webapp startup, and assistant startup scan"]]
+
+Note that since only one process can open port 4242 at a time, running
+more than one git-annex process with EKG support at the same time can
+result in some "resource busy (Address already in use)" messages -- but
+git-annex will continue to work.
diff --git a/doc/ekg/ekg.png b/doc/ekg/ekg.png
new file mode 100644
index 000000000..a8d16a2d8
--- /dev/null
+++ b/doc/ekg/ekg.png
diff --git a/doc/forum/A_question_an_the_nomad_use_cases:_files_to_fetch__44___files_to_delete__44___files_to_keep__63__/comment_1_fe291cd6cd8e2d5b8e23f8e3689d824b._comment b/doc/forum/A_question_an_the_nomad_use_cases:_files_to_fetch__44___files_to_delete__44___files_to_keep__63__/comment_1_fe291cd6cd8e2d5b8e23f8e3689d824b._comment
index 3eb2697a6..e29f57657 100644
--- a/doc/forum/A_question_an_the_nomad_use_cases:_files_to_fetch__44___files_to_delete__44___files_to_keep__63__/comment_1_fe291cd6cd8e2d5b8e23f8e3689d824b._comment
+++ b/doc/forum/A_question_an_the_nomad_use_cases:_files_to_fetch__44___files_to_delete__44___files_to_keep__63__/comment_1_fe291cd6cd8e2d5b8e23f8e3689d824b._comment
@@ -11,5 +11,5 @@ What you might be looking for is `git annex drop foo; rm foo`, followed by a git
 The assistant isn't really about only keeping a subset of files on your laptop. It would like to get them all, except for ones in \"archive\" directories.
 You can configure the assistant to use manual mode, and then it doesn't download any files on its own (so you have to manually `git annex get` them), but it will still handle all the other stuff the assistant does, like automatically committing and syncing changes.
 
-An archive repository wants one copy of every file that is not already stored in some other archive repository. So an archive repository could certianly be used instead of a transfer repository. (But not a small archive repository; those only want files that are moved to \"archive\" directories.) A better choice might be to make that server be a backup repository. That makes it want *every* file, no matter what, and it follows that it would archive everything, and have everything the client wants available for transferring to it.
+An archive repository wants one copy of every file that is not already stored in some other archive repository. So an archive repository could certainly be used instead of a transfer repository. (But not a small archive repository; those only want files that are moved to \"archive\" directories.) A better choice might be to make that server be a backup repository. That makes it want *every* file, no matter what, and it follows that it would archive everything, and have everything the client wants available for transferring to it.
 """]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository.mdwn b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository.mdwn
new file mode 100644
index 000000000..f09b2ea3d
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository.mdwn
@@ -0,0 +1,28 @@
+Hi!
+
+One of my annex repository has a very strange behavior. Every `git annex` command is very slow.
+
+I'm using MacOSX Mavericks, and this repository is a network drive, mounted with Samba. It's using direct mode, and the filesystem is crippled. I use *annex* for storing huge files, for example movies. I moved some files in this directory, and used `git annex add`. It was long (as checksum was performed) and I thought that everything was OK. I tried `git log -p`, it was OK too:
+
+    new file mode 120000
+    index 0000000..e58c65a
+    --- /dev/null
+    +++ b/Movies/movie.mp4
+    @@ -0,0 +1 @@
+    +../.git/annex/objects/FK/60/SHA256E-s346858581--053dca6a842376ab8022722df306ad5
+    \ No newline at end of file
+
+However it was not. I tried to launch `git annex sync another_repo` (with *another_repo* indirect and on a local disk) and it took ages. Even `git annex list` takes ages, **on every repository linked to this one**. With `ps -A`, I found out that the issue was created by `git --git-dir=/Volumes/SAMBA_REMOTE/.git --work-tree=/Volumes/SAMBA_REMOTE -c core.bare=false checkout -q -B annex/direct/master`.
+
+**Have you ever noticed this behavior? Have I done something wrong?**
+
+Here is the output of `git annex version`:
+
+    git-annex version: 5.20131117-gbd514dc
+    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi TDFA CryptoHash
+    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+    remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+    local repository version: 4
+    default repository version: 3
+    supported repository versions: 3 5
+    upgrade supported from repository versions: 0 1 2 4
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/bugs/direct_mode_sync_should_avoid_git_commit.mdwn b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/bugs/direct_mode_sync_should_avoid_git_commit.mdwn
new file mode 100644
index 000000000..ec7ce2cce
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/bugs/direct_mode_sync_should_avoid_git_commit.mdwn
@@ -0,0 +1 @@
+See [[/bugs/direct_mode_sync_should_avoid_git_commit/]] instead.
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_10_06dae5709750ea1da4f7fdbee4e84efc._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_10_06dae5709750ea1da4f7fdbee4e84efc._comment
new file mode 100644
index 000000000..c8feb05b9
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_10_06dae5709750ea1da4f7fdbee4e84efc._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 10"
+ date="2013-11-26T21:48:11Z"
+ content="""
+Hmm. Seems to me that `git commit` is trying to download the whole big file from the SMB share. Perhaps just to compare it with the symlink it expects to be there?
+
+When I try this, in a large direct mode repository with some video from *my* family, `git commit` does not open the file (verified with strace), let alone read it, and so finishes in well under 1 second. 
+
+Aha, I was able to reproduce `git commit` doing that with a repo on a FAT filesystem. git opens the file, and mmaps it, and I guess it proceeds to try to diff it against the symlink standin file it expected to be there.
+
+This is particularly unfortunate, since `git commit` is only, I think, doing this so that it can print out a \"Changes not staged for commit\" message. Which git-annex sync throws away. There seems to be no git commit option that disables this behavior.
+
+I think that this calls for making `git annex sync` not use `git commit` any longer, and instead manually build the commit using `git-write-tree` and `git-commit-tree`. Since I don't know if I will get to this before the thanksgiving holiday, I am creating a bug: [[bugs/direct_mode_sync_should_avoid_git_commit]]
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_11_2069c5c41882ae0a1973fb7da583b60e._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_11_2069c5c41882ae0a1973fb7da583b60e._comment
new file mode 100644
index 000000000..76ecd13c2
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_11_2069c5c41882ae0a1973fb7da583b60e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 11"
+ date="2013-11-26T21:57:52Z"
+ content="""
+Awesome! Thanks for your very efficient investigations. I'll stay tuned to the bug report.
+
+Happy Thanksgiving!
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_12_b35e3a87c30974eedd71ebe52ecbed96._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_12_b35e3a87c30974eedd71ebe52ecbed96._comment
new file mode 100644
index 000000000..282f1fb4c
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_12_b35e3a87c30974eedd71ebe52ecbed96._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 12"
+ date="2013-11-27T12:08:29Z"
+ content="""
+I corrected the bug address: See [[/bugs/direct_mode_sync_should_avoid_git_commit/]]
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_13_84e026f9bda87bfd12a3769dcef77f8b._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_13_84e026f9bda87bfd12a3769dcef77f8b._comment
new file mode 100644
index 000000000..dfc0db3d2
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_13_84e026f9bda87bfd12a3769dcef77f8b._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 13"
+ date="2013-11-27T12:13:04Z"
+ content="""
+thanks!
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_1_ed3534196164c6736a8dbf21c65c119d._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_1_ed3534196164c6736a8dbf21c65c119d._comment
new file mode 100644
index 000000000..ed104f488
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_1_ed3534196164c6736a8dbf21c65c119d._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T17:26:12Z"
+ content="""
+If you run git-annex with --debug, it will print out every command it is running. This is useful because A) I can see the commands in context and B) it includes timestamps, which is a little bit more informative than \"it took ages\". (Which can mean anything.)
+
+Anyway, I figured out the problem. Upgrade from v4 to v5 does what should be a one-time git checkout, but it seems that the auto upgrade code neglected to update annex.version, so it started doing it on every command run in a v4 repo. Fixed in git. You can work around the bug by running \"git config annex.version 5\".
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_2_1e29bcf568f02765c48f0eac6c640673._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_2_1e29bcf568f02765c48f0eac6c640673._comment
new file mode 100644
index 000000000..ab0cd9c9d
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_2_1e29bcf568f02765c48f0eac6c640673._comment
@@ -0,0 +1,45 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 2"
+ date="2013-11-26T20:42:03Z"
+ content="""
+My problem isn't solved. I cloned the repository from my netbook to the SMD drive, and added a file in this new direct annex repository :
+
+    [3singes:/Volumes/Video/Videos/Films] $ git annex add MyFamily.mkv --debug
+    [2013-11-26 19:52:59 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"ls-files\",\"--others\",\"--exclude-standard\",\"-z\",\"--\",\"MyFamily.mkv\"]
+    [2013-11-26 19:52:59 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"ls-files\",\"--modified\",\"-z\",\"--\",\"MyFamily.mkv\"]
+    [2013-11-26 19:52:59 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"cat-file\",\"--batch\"]
+    add MyFamily.mkv [2013-11-26 19:52:59 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"check-attr\",\"-z\",\"--stdin\",\"annex.backend\",\"annex.numcopies\",\"--\"]
+    (checksum...) [2013-11-26 19:52:59 CET] read: gsha256sum [\"MyFamily.mkv\"]
+    [2013-11-26 20:55:35 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"cat-file\",\"--batch\"]
+    [2013-11-26 20:55:35 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"hash-object\",\"-t\",\"blob\",\"-w\",\"--stdin\",\"--no-filters\"]
+    ok
+    (Recording state in git...)
+    [2013-11-26 20:55:35 CET] feed: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"update-index\",\"-z\",\"--index-info\"]
+    [2013-11-26 20:55:35 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"hash-object\",\"-w\",\"--stdin-paths\",\"--no-filters\"]
+    [2013-11-26 20:55:35 CET] feed: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"update-index\",\"-z\",\"--index-info\"]
+    [2013-11-26 20:55:35 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
+    [2013-11-26 20:55:36 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"write-tree\"]
+    [2013-11-26 20:55:36 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"commit-tree\",\"9bdb7b18b44020441ec8dc179e676120e769ff32\",\"-p\",\"refs/heads/git-annex\"]
+    [2013-11-26 20:55:37 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"update-ref\",\"refs/heads/git-annex\",\"293332232ca4e7428090171b52dcc5b3b80d1df6\"]
+
+Let's try to sync to my macbookpro annex repository:
+
+    [3singes:/Volumes/Video/Videos/Films] $ git annex sync macbookpro --debug
+    [2013-11-26 20:57:48 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"git-annex\"]
+    [2013-11-26 20:57:48 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
+    [2013-11-26 20:57:49 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..293332232ca4e7428090171b52dcc5b3b80d1df6\",\"--oneline\",\"-n1\"]
+    [2013-11-26 20:57:49 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..b2146cf0abc7d6a7e5c79d3b133181b56cd77461\",\"--oneline\",\"-n1\"]
+    [2013-11-26 20:57:49 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..c2cf7488b4745d4168491d8e62f5bdc354869133\",\"--oneline\",\"-n1\"]
+    [2013-11-26 20:57:49 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"cat-file\",\"--batch\"]
+    [2013-11-26 20:57:49 CET] read: git [\"config\",\"--null\",\"--list\"]
+    [2013-11-26 20:57:49 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"ls-files\",\"--stage\",\"-z\",\"--others\",\"--exclude-standard\",\"--\",\"/Volumes/Video/Videos\"]
+    [2013-11-26 20:57:50 CET] chat: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"cat-file\",\"--batch\"]
+    (Recording state in git...)
+    [2013-11-26 20:57:55 CET] feed: xargs [\"-0\",\"git\",\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"add\",\"-f\"]
+    commit
+    [2013-11-26 20:57:55 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"commit\",\"-m\",\"git-annex automatic sync\"]
+
+Now it's 21:41 CET, and it's been stuck for circa 1 hour.
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_3_9ea6803a94b1de15079a3fa20d59c9af._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_3_9ea6803a94b1de15079a3fa20d59c9af._comment
new file mode 100644
index 000000000..f2c4fd77e
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_3_9ea6803a94b1de15079a3fa20d59c9af._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 3"
+ date="2013-11-26T20:51:59Z"
+ content="""
+The problem you reported *is* solved. You were not talking about syncing before.
+
+If your setup is such that `git commit` takes a long time to run, then `git annex sync` is also necessarily going to take a long time to run.
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_4_3fae5a7fa5d99d0eb4473adb43e7f6f5._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_4_3fae5a7fa5d99d0eb4473adb43e7f6f5._comment
new file mode 100644
index 000000000..e9b7655cf
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_4_3fae5a7fa5d99d0eb4473adb43e7f6f5._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 4"
+ date="2013-11-26T20:55:39Z"
+ content="""
+Thanks for your answer. On the second part of my problem, *why* should `git commit` be slow? It's only committing a file with a line (../.git/annex/...), isn't it?
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_5_57a5b73cff480266355e75c7bdc762c2._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_5_57a5b73cff480266355e75c7bdc762c2._comment
new file mode 100644
index 000000000..51e31d9b4
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_5_57a5b73cff480266355e75c7bdc762c2._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 5"
+ date="2013-11-26T21:02:17Z"
+ content="""
+Err, I read my post again, and I definitely *was* talking about syncing ;-)
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_6_bbcf5e863c8f152e1079536e9011a404._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_6_bbcf5e863c8f152e1079536e9011a404._comment
new file mode 100644
index 000000000..4640a91bf
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_6_bbcf5e863c8f152e1079536e9011a404._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 6"
+ date="2013-11-26T21:04:44Z"
+ content="""
+I think the most likely reason for git commit to be slow on your setup is that it probably rewrites .git/index. If you have a lot of files in your repository, the index file will be large and rewriting the index file will involve re-transferring it all over the network to the SMB share. 
+
+It's also possible that git commit scans the whole work tree, although I don't think it should -- it's not been told to with -a.
+
+You may be able to find what's taking a long time by
+
+    strace git --git-dir=/Volumes/Video/Videos/.git --work-tree=/Volumes/Video/Videos -c core.bare=false commit -m \"git-annex automatic sync\"
+
+(or ltrace)
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_7_fdcd144c22601bdf98ff844254b0120d._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_7_fdcd144c22601bdf98ff844254b0120d._comment
new file mode 100644
index 000000000..033a1af45
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_7_fdcd144c22601bdf98ff844254b0120d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 7"
+ date="2013-11-26T21:07:12Z"
+ content="""
+If you kept your git repository on your local disk, and used a [[directory special remote|special_remotes/directory]] on the SMB share, you could then `git annex copy --to smbshare` and `git annex get --from smbshare` as desired, which would probably be much more efficient.
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_8_b77243e765b2af7ba71e963fcb5cbbb1._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_8_b77243e765b2af7ba71e963fcb5cbbb1._comment
new file mode 100644
index 000000000..273b9d8e9
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_8_b77243e765b2af7ba71e963fcb5cbbb1._comment
@@ -0,0 +1,71 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 8"
+ date="2013-11-26T21:17:38Z"
+ content="""
+Thanks again for your answers.
+
+`.git/index` is only 30Ko big. It shouldn't be an issue, even through the network.
+
+However, I ran `lsof`, and strangely it lock the big file I added before (`/Volumes/Video/Videos/Films/MyFamily.mkv`)
+
+    COMMAND   PID    USER   FD   TYPE DEVICE    SIZE/OFF                 NODE NAME
+    git     68047 3singes  cwd    DIR   46,7       16384  5152641528667254045 /Volumes/Video/Videos
+    git     68047 3singes  txt    REG    1,4     3035984             77501447 /Applications/git-annex.app/Contents/MacOS/bundle/git
+    git     68047 3singes  txt    REG   46,7        8632  9219631544499731818 /Volumes/Video/Videos/.git/objects/pack/pack-99901c82bacfa26c04f505ceb27c4af9ccda414f.idx
+    git     68047 3singes  txt    REG    1,4      403392             77501680 /Applications/git-annex.app/Contents/MacOS/bundle/usr/lib/libpcre.0.dylib
+    git     68047 3singes  txt    REG   46,7        4012  8204150806531008435 /Volumes/Video/Videos/.git/objects/pack/pack-bb60a2315b13bda720682a4213507e5ee9ba029f.idx
+    git     68047 3singes  txt    REG   46,7       15969 12003107822997399035 /Volumes/Video/Videos/.git/objects/pack/pack-bb60a2315b13bda720682a4213507e5ee9ba029f.pack
+    git     68047 3singes  txt    REG    1,4      169392             77501683 /Applications/git-annex.app/Contents/MacOS/bundle/usr/lib/libz.1.dylib
+    git     68047 3singes  txt    REG    1,4     2088992             77501673 /Applications/git-annex.app/Contents/MacOS/bundle/usr/lib/libiconv.2.dylib
+    git     68047 3singes  txt    REG    1,4      600832             72809225 /usr/lib/dyld
+    git     68047 3singes  txt    REG    1,4   342937194             75930310 /private/var/db/dyld/dyld_shared_cache_x86_64
+    git     68047 3singes    0u   CHR  16,10    0t718314                 2413 /dev/ttys010
+    git     68047 3singes    1w   CHR    3,2         0t0                  308 /dev/null
+    git     68047 3singes    2w   CHR    3,2         0t0                  308 /dev/null
+    git     68047 3singes    3u   REG   46,7           0 17793593705208135594 /Volumes/Video/Videos/.git/index.lock
+    git     68047 3singes    4r   REG   46,7 15581987050 12221620371912261305 /Volumes/Video/Videos/Films/MyFamily.mkv
+    git     68047 3singes    8w   CHR    3,2         0t0                  308 /dev/null
+
+I'm using MacOSX, so I can only use `dtrace`, which I don't know so much.
+
+**The process is over, after 1H30:**
+
+    ok
+    [2013-11-26 22:13:48 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"symbolic-ref\",\"HEAD\"]
+    [2013-11-26 22:13:48 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"refs/heads/annex/direct/master\"]
+    [2013-11-26 22:13:48 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--verify\",\"-q\",\"refs/heads/synced/master\"]
+    [2013-11-26 22:13:49 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/annex/direct/master..refs/heads/synced/master\",\"--oneline\",\"-n1\"]
+    pull macbookpro
+    [2013-11-26 22:13:49 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"fetch\",\"macbookpro\"]
+    From /Users/3singes/Movies/NE PAS SAUVEGARDER/Videos
+       b2146cf..c2cf748  git-annex  -> macbookpro/git-annex
+    [2013-11-26 22:13:50 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--verify\",\"-q\",\"refs/remotes/macbookpro/annex/direct/master\"]
+    [2013-11-26 22:13:50 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--verify\",\"-q\",\"refs/remotes/macbookpro/synced/master\"]
+    [2013-11-26 22:13:50 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/synced/master..refs/remotes/macbookpro/synced/master\",\"--oneline\",\"-n1\"]
+    ok
+    [2013-11-26 22:13:50 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"git-annex\"]
+    [2013-11-26 22:13:50 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
+    [2013-11-26 22:13:50 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..293332232ca4e7428090171b52dcc5b3b80d1df6\",\"--oneline\",\"-n1\"]
+    [2013-11-26 22:13:51 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..b2146cf0abc7d6a7e5c79d3b133181b56cd77461\",\"--oneline\",\"-n1\"]
+    [2013-11-26 22:13:51 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..c2cf7488b4745d4168491d8e62f5bdc354869133\",\"--oneline\",\"-n1\"]
+    [2013-11-26 22:13:51 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"branch\",\"-f\",\"synced/master\"]
+    [2013-11-26 22:13:51 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"branch\",\"-f\",\"master\"]
+    [2013-11-26 22:13:51 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--verify\",\"-q\",\"refs/remotes/macbookpro/synced/master\"]
+    [2013-11-26 22:13:51 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/remotes/macbookpro/synced/master..refs/heads/synced/master\",\"--oneline\",\"-n1\"]
+    [2013-11-26 22:13:51 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"show-ref\",\"--verify\",\"-q\",\"refs/remotes/macbookpro/git-annex\"]
+    [2013-11-26 22:13:51 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"log\",\"refs/remotes/macbookpro/git-annex..git-annex\",\"--oneline\",\"-n1\"]
+    push macbookpro
+    [2013-11-26 22:13:52 CET] call: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"push\",\"macbookpro\",\"+git-annex:synced/git-annex\",\"annex/direct/master:synced/master\"]
+    Counting objects: 9, done.
+    Delta compression using up to 8 threads.
+    Compressing objects: 100% (4/4), done.
+    Writing objects: 100% (5/5), 440 bytes | 0 bytes/s, done.
+    Total 5 (delta 3), reused 0 (delta 0)
+    To /Users/3singes/Movies/NE PAS SAUVEGARDER/Videos
+       c2cf748..2933322  git-annex -> synced/git-annex
+    [2013-11-26 22:13:57 CET] read: git [\"--git-dir=/Volumes/Video/Videos/.git\",\"--work-tree=/Volumes/Video/Videos\",\"-c\",\"core.bare=false\",\"push\",\"macbookpro\",\"master\"]
+    ok
+
+"""]]
diff --git a/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_9_cb0815e96ee211d4778f2e7a4274e855._comment b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_9_cb0815e96ee211d4778f2e7a4274e855._comment
new file mode 100644
index 000000000..041f3c547
--- /dev/null
+++ b/doc/forum/Actions_very_slow_on_a_direct___40__and_crippled__41___annex_repository/comment_9_cb0815e96ee211d4778f2e7a4274e855._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 9"
+ date="2013-11-26T21:19:42Z"
+ content="""
+I thought to a directory special remote, but it doesn't meet my needs: the SMB drive is used by a MediaCenter, so I need the working tree.
+"""]]
diff --git a/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository.mdwn b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository.mdwn
new file mode 100644
index 000000000..c126f8373
--- /dev/null
+++ b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository.mdwn
@@ -0,0 +1,17 @@
+Hi!
+
+What is the best way to add again the content of file in an direct and crippled annex repository? I'm using such a repository on a SMB drive, with no symbolic links, that's why the repository is in direct mode.
+
+For example:
+
+`/disk/annex-rep/a.bin` contains the text `../.git/annex/objects/W3/M8/SHA256E-s4701522386--e486cce01b1870cee394a376a3acc64a608e84e38b85e6c21c29721cf14328e6.bin/SHA256E-s4701522386--e486cce01b1870cee394a376a3acc64a608e84e38b85e6c21c29721cf14328e6.bin`
+
+and I've got the real content in another directory, outside annex: /disk/a.bin (contains the binary data)
+
+I imagined this process:
+* replace `/disk/annex-rep/a.bin` with `/disk/a.bin``
+* update `git-annex:122/4b8/SHA256E-s4701522386--e486cce01b1870cee394a376a3acc64a608e84e38b85e6c21c29721cf14328e6.bin.log` by adding this repository uuid
+
+I tried `git annex reinject` but it didn't work.
+
+Is there another way?
diff --git a/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_1_552e74f9573a34ec178f396b83252c3e._comment b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_1_552e74f9573a34ec178f396b83252c3e._comment
new file mode 100644
index 000000000..439c985dc
--- /dev/null
+++ b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_1_552e74f9573a34ec178f396b83252c3e._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T19:54:21Z"
+ content="""
+There's a bug report asking that reinject work in direct mode. I just have not gotten around to it.
+
+Another way to do it would be to make a temp directory in your annex repository, move or copy the file to there, and `git annex add`. As long as you're not using the WORM backend, the checksum will be used, and so it'll see it's added the content of the file, and make the a.bin file have that content too.
+
+Off to see if I can easily add direct mode reinject now..
+"""]]
diff --git a/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_2_33c57922714f204fc63c260b838f3712._comment b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_2_33c57922714f204fc63c260b838f3712._comment
new file mode 100644
index 000000000..afc449ac2
--- /dev/null
+++ b/doc/forum/Best_way_to_re-add_a_file_in_a_direct_and_crippled_annex_repository/comment_2_33c57922714f204fc63c260b838f3712._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 2"
+ date="2013-11-26T20:18:56Z"
+ content="""
+Turned out to be trivial, so it's supported now.
+"""]]
diff --git a/doc/forum/Change_remote_server_address/comment_1_401c3d2530ac7ba41dd3857ab4737ed5._comment b/doc/forum/Change_remote_server_address/comment_1_401c3d2530ac7ba41dd3857ab4737ed5._comment
new file mode 100644
index 000000000..d4e406829
--- /dev/null
+++ b/doc/forum/Change_remote_server_address/comment_1_401c3d2530ac7ba41dd3857ab4737ed5._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-01T16:35:47Z"
+ content="""
+Yes, you can certainly edit .git/config in any way you like and the assistant will use the new values when started back up.
+
+It shouldn't be using a hardcoded IP address normally, unless you manually entered an IP address when setting up that ssh remote. Using DNS is better..
+"""]]
diff --git a/doc/forum/Effectively_replicating_backup_files.mdwn b/doc/forum/Effectively_replicating_backup_files.mdwn
new file mode 100644
index 000000000..85d8f4b52
--- /dev/null
+++ b/doc/forum/Effectively_replicating_backup_files.mdwn
@@ -0,0 +1,25 @@
+I currently use duply/duplicity to back up my networked computers to my home server. I have two external HDDs and, every week or so, I bring one of these home and copy the backup files to the hard drive (I leave them on the server to easily restore files and because I have a large hard drive in that). I use some hand-written scripts to keep a copy these backup files in the cloud (Ubuntu One) until they have been copied to both hard drives, ensuring that there are always two copies of the files somewhere offsite. Out of paranoia, I also have some "standalone backups" that are just huge encrypted archives of important folders (say, my entire Photos directory) as at a certain date - in case for some reason duplicity ever stops working or I need to roll something back to a version years earlier. I am less worried about these standalone backups and manually keep one copy of each somewhere.
+
+It sounds like Git-Annex could automate things quite nicely (and give me some neat extras, like knowing where they were). This is how I understand I should do it, but please let me know if it is the right approach or if you have any suggestions:
+
+1. Create a folder on my server called "annex" and make a Git-Annex "large backup" repository in there.
+2. Create a folder within that called "archive" and put a "backup" folder within that. I understand that having the backups within an archive folder will mean that they aren't automatically copied to my desktop machines etc. 
+3. Within that "backup" folder, create two folders, one called "duplicity" and one called "standalone". Put the backups in the respective folders.
+4. Set up gcrypt Git-Annex repositories on my two external HDDs as "small backups". This seems to just start copying files across. That surprised me, as the files are in the archive folder and I thought the default was numcopies=1. Is there some autosync option that I need to turn off? Ideally, I would like it to encrypt/decrypt primarily with my server GPG key (which I'm not worried about copying around my computers), but also encrypt to my personal GPG key (where I'd only put my public key on the server, but I know I will not lose the secret key for that). Am I right that to do that I would need to set the repos up manually with:
+
+    git init --bare /mnt/externalHDD1
+
+    git annex initremote externalHDD1 type=gcrypt gitrepo=/mnt/externalHDD1 keyid=$serverkey keyid=$personalkey
+
+    git annex sync externalHDD1
+
+    Or should the gitrepo be the location of my main Git-Annex repository? How do I make it sync up with my other repos?
+
+5. I understand that I would then need to set numcopies=3 in a .gitattributes file in the "archive/backup/duplicity" directory and, say, a numcopies=2 in the "archive/backup/standalone".
+6. I could then add a cloud repository as a "transfer" repository and Git-Annex should only keep files on that that are not already in the right number of places (similar to what my scripts are doing now).
+7. I have recently upgraded my hard drive, so I have my old 1TB internal hard drive that I will be putting in a cupboard somewhere. I was thinking that I could make this an archive drive for things like one copy of my duplicity/standalone backups. I wouldn't want it to be the only copy of anything. If I just set it as an archive drive, would this work?
+8. Are there more clever ways of doing this? I consider my external HDDs and the cloud repo as "offsite" repositories and ideally there would always be one copy of my backups offsite (in addition to at least three overall). There would also ideally be one of each of my files "live" (in most cases my server) that could instantly push files into a cloud repo and then to wherever I am. Is there any ability to put repositories in groups and write rules like that?
+
+Any thoughts greatly appreciated!
+
+Aaron
diff --git a/doc/forum/Effectively_replicating_backup_files/comment_1_b1ab0da82db076c5244b0dcc95282ddd._comment b/doc/forum/Effectively_replicating_backup_files/comment_1_b1ab0da82db076c5244b0dcc95282ddd._comment
new file mode 100644
index 000000000..54f7f782a
--- /dev/null
+++ b/doc/forum/Effectively_replicating_backup_files/comment_1_b1ab0da82db076c5244b0dcc95282ddd._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-07T16:42:14Z"
+ content="""
+This all sounds reasonable to me.
+
+gitrepo= is the location of the repository you are setting up with gcrypt, not your existing git-annex repository.
+
+numcopies configures the lower bound of the number of copies, not the upper bound. There's no \"small backup\" type, you must mean either small archive, or incremental backup. Either type of repository is going to want to have files that have not previously been archived, or backed up.
+
+You might eventually want to write your own [[preferred_content]] expressions to handle offsite repositories. I'd recommend starting simple and building up.
+"""]]
diff --git a/doc/forum/Effectively_replicating_backup_files/comment_2_472ab9c973b475f7f3ce7e3934f94281._comment b/doc/forum/Effectively_replicating_backup_files/comment_2_472ab9c973b475f7f3ce7e3934f94281._comment
new file mode 100644
index 000000000..668416c04
--- /dev/null
+++ b/doc/forum/Effectively_replicating_backup_files/comment_2_472ab9c973b475f7f3ce7e3934f94281._comment
@@ -0,0 +1,19 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnFjuvfPpi1kf6l54bxfFUm0Aw_Gf_IO0o"
+ nickname="Aaron"
+ subject="comment 2"
+ date="2013-11-07T19:46:32Z"
+ content="""
+Thanks Joey!
+
+> gitrepo= is the location of the repository you are setting up with gcrypt, not your existing git-annex repository.
+
+Great, thanks. If I set these up outside of the WebApp, what is the best way to link them up to my main repositories?
+
+> numcopies configures the lower bound of the number of copies, not the upper bound. There's no \"small backup\" type, 
+> you must mean either small archive, or incremental backup. Either type of repository is going to want to have files 
+> that have not previously been archived, or backed up.
+
+Yes, I meant incremental backup. Thanks, understood. The page on preferred content ( http://git-annex.branchable.com/preferred_content/ ) made things a bit clearer. I didn't realise that the incremental backups etc want a copy even if it isn't necessary to satisfy numcopies. Does that mean that once it is on one backup drive, it will not be sent to the other unless I increase numcopies?
+
+"""]]
diff --git a/doc/forum/Effectively_replicating_backup_files/comment_3_826493bd59b81786c1f6a56f1c438004._comment b/doc/forum/Effectively_replicating_backup_files/comment_3_826493bd59b81786c1f6a56f1c438004._comment
new file mode 100644
index 000000000..9088de9e7
--- /dev/null
+++ b/doc/forum/Effectively_replicating_backup_files/comment_3_826493bd59b81786c1f6a56f1c438004._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 3"
+ date="2013-11-08T17:06:02Z"
+ content="""
+The webapp can use remotes that you have configured at the command line just as well as it can use remotes you configure using the webapp.
+
+Each file only gets backed up to one incremental backup repository. If you have a full backup repository it will (try to) get another copy of every single file.
+"""]]
diff --git a/doc/forum/GPG_passphrase_handling.txt b/doc/forum/GPG_passphrase_handling.txt
index 6b141bba4..b0f82cb89 100644
--- a/doc/forum/GPG_passphrase_handling.txt
+++ b/doc/forum/GPG_passphrase_handling.txt
@@ -1,3 +1,5 @@
+[[!meta title="GPG passphrase handling on OSX"]]
+
 Hello!
 I'm using OSX 10.9 and have installed gpg (and gpg2, if it matters) through
 homebrew and git-annex through cabal. I also installed
diff --git a/doc/forum/GPG_passphrase_handling/comment_3_84eb129c8483b87b3ae6ecaf8b4a8309._comment b/doc/forum/GPG_passphrase_handling/comment_3_84eb129c8483b87b3ae6ecaf8b4a8309._comment
new file mode 100644
index 000000000..298e2f13d
--- /dev/null
+++ b/doc/forum/GPG_passphrase_handling/comment_3_84eb129c8483b87b3ae6ecaf8b4a8309._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T20:39:36Z"
+ content="""
+There seem to be a lot of different ways to install gpg on OSX, with different results in what works and not. I don't know what's going on with that. Advice from those who understand Mac OS would be appreciated.
+
+As far as the \"gpg: no valid addressees\" bug goes, I can reproduce it on Linux, and have fixed it. Only affected using gcrypt with encryption=pubkey.
+
+(Please file bug reports in [[bugs]] in the future, not in the forum!)
+"""]]
diff --git a/doc/forum/GPG_passphrase_handling/comment_4_8724297f6d7ac140ab395a940bab0d7d._comment b/doc/forum/GPG_passphrase_handling/comment_4_8724297f6d7ac140ab395a940bab0d7d._comment
new file mode 100644
index 000000000..983c35c3a
--- /dev/null
+++ b/doc/forum/GPG_passphrase_handling/comment_4_8724297f6d7ac140ab395a940bab0d7d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkzwmw_zyMpZC9_J7ey--woeYPoZkAOgGw"
+ nickname="dxtrish"
+ subject="comment 4"
+ date="2013-11-03T13:10:11Z"
+ content="""
+I would have filed it in the bug section if I knew it was a bug. I just thought I had done something wrong :)
+"""]]
diff --git a/doc/forum/Git_annex___39__corrupting__39___itself.mdwn b/doc/forum/Git_annex___39__corrupting__39___itself.mdwn
new file mode 100644
index 000000000..fe1edc17d
--- /dev/null
+++ b/doc/forum/Git_annex___39__corrupting__39___itself.mdwn
@@ -0,0 +1,34 @@
+Hi,
+
+Since the I updated to `2013-10-24` `git annex` has corrupted itself twice on my setup.  I'm not claiming causality here and thus I haven't filled it as a bug (probably the mistake is mine).
+
+I use three laptops and one remote ssh server.  The motherboard on laptop *T* seems to have broken and I haven't fixed it yet.  I have disabled sync to *T*  on the webapp dashboard.  
+
+First, one computer, called *W*, broke on Friday.  I got the dreaded [serious problem](http://git-annex.branchable.com/devblog/day_41__onward/) screen. `git fsck` reported lots of missing blobs and tree problem, though my data seemed OK.  I git cloned the repo from computer *X*.  Now, last night both X and W reported the same problem (log below).  *W*  recovered itself somehow, but *X*  is now in a cycle of re-adding all files in the repo and the posting the below error that has to do with computer *T* (IP ending with 107).  
+
+I would appreciate hints on why this suddenly started happen.  Computer T has been out of sync for almost 14 days (since the 24th of October I think).
+
+    error: refs/remotes/192.168.1.107_annex/git-annex does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/master does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/synced/git-annex does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/synced/master does not point to a valid object!
+    error: refs/synced/2ed58ecf-8e8c-44b8-ad34-d42ddfb35315/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/git-annex does not point to a valid object!
+    error: refs/synced/2ed58ecf-8e8c-44b8-ad34-d42ddfb35315/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/master does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/git-annex does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/master does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/git-annex does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/master does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/git-annex does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/master does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/synced/git-annex does not point to a valid object!
+    error: refs/remotes/192.168.1.107_annex/synced/master does not point to a valid object!
+    error: refs/synced/2ed58ecf-8e8c-44b8-ad34-d42ddfb35315/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/git-annex does not point to a valid object!
+    error: refs/synced/2ed58ecf-8e8c-44b8-ad34-d42ddfb35315/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/master does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/git-annex does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/cmFzbXVzQGNvZGVyb2xsZXJzLmNvbQ==/master does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/git-annex does not point to a valid object!
+    error: refs/synced/f54b8200-8ec1-43d2-8710-b73ec118addc/master does not point to a valid object!
+    error: invalid object 100644 1ca66de3cdd9c79cde26a7555cf3b8d26d0e371d for '000/147/SHA256E-s347--1ab8084bf9ae06407ce0a7260a83638ea6e9a028dc59b4815fd60aec61dbd747.txt.log.log'
+    fatal: git-write-tree: error building trees
+    TransferScanner crashed: failed to read sha from git write-tree
+    [2013-11-04 09:45:41 CET] TransferScanner: warning TransferScanner crashed: failed to read sha from git write-tree
diff --git a/doc/forum/Git_annex___39__corrupting__39___itself/comment_1_bcf50a215e2f8771e098aadfff4c300c._comment b/doc/forum/Git_annex___39__corrupting__39___itself/comment_1_bcf50a215e2f8771e098aadfff4c300c._comment
new file mode 100644
index 000000000..2fe95ab33
--- /dev/null
+++ b/doc/forum/Git_annex___39__corrupting__39___itself/comment_1_bcf50a215e2f8771e098aadfff4c300c._comment
@@ -0,0 +1,43 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlEXAlu8qKv_FHYOv-uEohdGgMY_Lw-Ges"
+ nickname="Jonas"
+ subject="Just happened for me as well."
+ date="2013-11-12T08:10:56Z"
+ content="""
+This was the first search result when I googled the error message, I'm not sure what has happened (or if it is a problem since I don't change my files that often).
+
+git-annex version: 4.20131101
+
+Also running git annex with one ssh remote ( laptop1 & laptop2 synching through a ssh remote server ).
+
+Got a bunch of 
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/git-annex does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/master does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/git-annex does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/master does not point to a valid object!
+when I tried a manual git annex sync, and noticed that I had a bunch of those in the log in the webapp as well... 
+
+The gui doesn't show that anything is wrong, and looking at the log it seems that things are atleast uploading
+
+    [2013-11-12 09:05:46 CET] Committer: Committing changes to git
+    [2013-11-12 09:05:46 CET] Pusher: Syncing with born 
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/git-annex does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/master does not point to a valid object!
+    Everything up-to-date
+
+    FILE
+
+       32768  42%    0.00kB/s    0:00:00  
+       76972 100%   42.16MB/s    0:00:00 (xfer#1, to-check=0/1)
+
+    sent 77056 bytes  received 31 bytes  51391.33 bytes/sec
+    total size is 76972  speedup is 1.00
+    [2013-11-12 09:05:48 CET] Transferrer: Uploaded FILE
+    [2013-11-12 09:05:48 CET] Pusher: Syncing with born 
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/git-annex does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/master does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/git-annex does not point to a valid object!
+    error: refs/synced/dbb70cea-4b83-416f-93af-e59082c4d633/master does not point to a valid object!
+    To ssh://me@born/annex
+      54e04cf..333cf10  git-annex -> synced/git-annex
+"""]]
diff --git a/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_75f957e7be6c1ad8936c0a2a5374db3e._comment b/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_75f957e7be6c1ad8936c0a2a5374db3e._comment
new file mode 100644
index 000000000..80f778bb1
--- /dev/null
+++ b/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_75f957e7be6c1ad8936c0a2a5374db3e._comment
@@ -0,0 +1,20 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlEXAlu8qKv_FHYOv-uEohdGgMY_Lw-Ges"
+ nickname="Jonas"
+ subject="comment 3"
+ date="2013-11-13T09:03:24Z"
+ content="""
+I did a change of one of the files and that totally broke all other repositories, git fsck reports a lot of missing trees (I'm not sure if it is normal), and git annex fsck started reporting invalid object for another file for some reason, also got a (git annex repair still reports everything is fine though.)
+
+    fatal: git-write-tree: error building trees
+    git-annex: failed to read sha from git write-tree
+
+
+
+I tried following those instructions but I don't think I had a good repository, git annex repair reported everything was ok but git fsck said a lot of trees where missing and it stopped updating.
+I noticed I was running different git version (git version 1.7.9.5 on the server and git version 1.8.4.2 on one of the clients), so maybe that was part of the reason.
+
+I couldn't find out what remote dbb70cea-4b83-416f-93af-e59082c4d633 was supposed to be either, it wasn't any of the active ones and it didn't show up with git annex status either (I've lost a few repositories when I reinstalled my computer).
+
+I ended up recreating the repository (by copying the raw files) from what I think is the most recent version from one of my computers and hope that it was a error that happened due to upgrades.
+"""]]
diff --git a/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_ab062b1df3b55fd49852a6220c98249e._comment b/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_ab062b1df3b55fd49852a6220c98249e._comment
new file mode 100644
index 000000000..76e9d00de
--- /dev/null
+++ b/doc/forum/Git_annex___39__corrupting__39___itself/comment_3_ab062b1df3b55fd49852a6220c98249e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 3"
+ date="2013-11-12T17:19:32Z"
+ content="""
+I have been getting this too. Here is what I have done to fix it:
+
+[[tips/recovering_from_a_corrupt_git_repository]]
+"""]]
diff --git a/doc/forum/Help_on_my_usecase.mdwn b/doc/forum/Help_on_my_usecase.mdwn
new file mode 100644
index 000000000..ef670aa25
--- /dev/null
+++ b/doc/forum/Help_on_my_usecase.mdwn
@@ -0,0 +1,22 @@
+I am using git-annex assistant for a few months now and still don't think I have it all setup correctly. My setup is:
+
+* Laptop Computer with low storage. Content creator, assistant: file source
+* Desktop Computer with medium storage capacity. Consumer, assistant: manual Mode
+* 2TB USB HD (EXT4) Backup, assistant: full backup
+* 2.5" portable 500GB drive NTFS formatted. transfer to backup: assistant: tried transfer and partial backup
+* Root Server on the web, not yet in the mix. Planned: Index only / content creator
+
+My primary goal is getting the stuff from the Laptop to the 2TB USB drive, syncing the annex with the desktop so I can get files on the desktop from the backup.
+What works:
+
+* Checking stuff into the annex on the Laptop
+* When the 2TB drive is connected to the Laptop, stuff is automatically moved there too
+* Bare Repo on the 2.5" configured as partial backup automatically backups the data
+
+What doesn't work:
+
+* Connecting the 2.5" bare repo to the Desktop to move stuff to the backup drive automatically
+* Having a human readable folder Structure on the 2.5" NTFS drive. I'd be ok to have a bare repo plus a special remote on the drive, but I don't know how to configure it
+* How do I drop stuff from the bare repo on the 2.5" drive? I think a partial backup should drop content that is in a full backup, but it doesn't
+
+Thanks for reading this long post. If anyone has any tips on how to configure the assistant, thats much appreciated.
diff --git a/doc/forum/Help_on_my_usecase/comment_1_a35b35c7927640f21d47c3df4f91dabb._comment b/doc/forum/Help_on_my_usecase/comment_1_a35b35c7927640f21d47c3df4f91dabb._comment
new file mode 100644
index 000000000..25116a7c4
--- /dev/null
+++ b/doc/forum/Help_on_my_usecase/comment_1_a35b35c7927640f21d47c3df4f91dabb._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-09T18:18:49Z"
+ content="""
+An incremental backup is supposed to drop content once it reaches a full backup. But, the assistant can only do that if it's able to verify that the full backup drive (or some other repository it can access) has a file, at the same time it's dropping it from the incremental backup drive. If you don't have both the incremental and full backup drives plugged in at the same time, you could consider making git-annex [[trust]] the full backup drive, which would avoid this explicit check.
+
+It sounds like you want a non-bare git repository on the 2.5\" drive. The assistant does not currently support setting that up, but you can do it by just using `git clone` as shown in the [[walkthrough]].
+
+I'm not clear on what doesn't work when you connect the 2.5\" drive to your desktop.
+"""]]
diff --git a/doc/forum/How_does_one_change_git-annex_assistant__39__s_web_browser__63__/comment_6_799b9d9d3ffbc2c14eca8d442e2aff8c._comment b/doc/forum/How_does_one_change_git-annex_assistant__39__s_web_browser__63__/comment_6_799b9d9d3ffbc2c14eca8d442e2aff8c._comment
new file mode 100644
index 000000000..767426fef
--- /dev/null
+++ b/doc/forum/How_does_one_change_git-annex_assistant__39__s_web_browser__63__/comment_6_799b9d9d3ffbc2c14eca8d442e2aff8c._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
+ nickname="Carlo"
+ subject="comment 6"
+ date="2013-11-15T13:43:06Z"
+ content="""
+Since git web--browse defaults to firefox on my system (Ubuntu/XMonad), I did this on Ubuntu to get the system default browser.
+
+  git config --global web.browser xdg-open
+
+"""]]
diff --git a/doc/forum/How_to_cancel_an_add__63__.mdwn b/doc/forum/How_to_cancel_an_add__63__.mdwn
new file mode 100644
index 000000000..e0b0f1c8f
--- /dev/null
+++ b/doc/forum/How_to_cancel_an_add__63__.mdwn
@@ -0,0 +1,5 @@
+What is the safest way to cancel a `git annex add` before the first commit?
+
+Say I first added a directory with a lot of small files to the annex and then (while watching the endless list of checksum operations) decide I should actually put them in a tar file and annex that instead.
+
+The problem seems to be that `git annex add` immediately replaces the files with symlinks instead of waiting for a commit, so I can't just `git reset largedir/; tar cvfz largedir.tgz largedir/; git annex add largedir.tgz`.
diff --git a/doc/forum/How_to_cancel_an_add__63__/comment_1_f768ce5dc7c76f96ee6eb352f167be44._comment b/doc/forum/How_to_cancel_an_add__63__/comment_1_f768ce5dc7c76f96ee6eb352f167be44._comment
new file mode 100644
index 000000000..cef938469
--- /dev/null
+++ b/doc/forum/How_to_cancel_an_add__63__/comment_1_f768ce5dc7c76f96ee6eb352f167be44._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-03T00:50:48Z"
+ content="""
+Run `git annex unannex` on the files.
+"""]]
diff --git a/doc/forum/Manual_Setup_of_a_Central_Repo/comment_1_3a163fd5629dc40423f1290a78ae1c07._comment b/doc/forum/Manual_Setup_of_a_Central_Repo/comment_1_3a163fd5629dc40423f1290a78ae1c07._comment
index 7fe30c6dd..e5630b331 100644
--- a/doc/forum/Manual_Setup_of_a_Central_Repo/comment_1_3a163fd5629dc40423f1290a78ae1c07._comment
+++ b/doc/forum/Manual_Setup_of_a_Central_Repo/comment_1_3a163fd5629dc40423f1290a78ae1c07._comment
@@ -4,7 +4,7 @@
  subject="comment 1"
  date="2013-08-26T18:46:06Z"
  content="""
-You could certianly do that. I don't think it's the easiest way.
+You could certainly do that. I don't think it's the easiest way.
 
 Note that this is essentially a git question. It really has nothing to do with git-annex, unless you want to use the git-annex assistant, which can sync a repository over XMPP without needing a central git repository at all.
 
diff --git a/doc/forum/New_special_remote_suggeston_-_clean_directory.mdwn b/doc/forum/New_special_remote_suggeston_-_clean_directory.mdwn
new file mode 100644
index 000000000..9fd3c5a20
--- /dev/null
+++ b/doc/forum/New_special_remote_suggeston_-_clean_directory.mdwn
@@ -0,0 +1,15 @@
+The [[special remotes]] available all do great things and enable a ton of different services to be integrated.
+
+Strikingly, the one service I can't satisfactorily integrate with git-annex is a remote folder on a eg NAS (think: computer without git-annex installed) that I want to look like the original annex. As in, when I do a 'tree annexdir' it'd look the same on both locations (except, on the remote there would not be any symlinks, it'd be like it was in directmode, and there would not be a .git subdir).
+
+## Why? Use Case?
+
+I have a Synology NAS that I share access with with my wife. I want her to be able to access the files (photos/videos/music) in a sane manner (ie: not traversing sub-sub-sub 'randomly' named directories) but I also want to be able to manage them with git-annex on my machine (to gain the standard git-annex benefits, specifically the bob the archivist use case). The NAS has the ability to use ssh+rsync, so I'll assume those two tools can be used.
+
+This special remote could be thought of as the 'least common denominator of special remotes'; almost any server with ssh+rsync could be a remote, no matter if you have install privs or if the architecture (eg: ARM) is supported by git-annex.
+
+## Issues?
+
+First and foremost, this can't be (really really shouldn't be) a trusted remote; my wife could accidentally delete all files on the NAS while I am away. So my local git-annex shouldn't assume the NAS counts towards numcopies (unless I'm a real masochist).
+
+Secondly, what to do when files change/are added/removed on the special remote? Probably the same thing that the assistant does with everything. The only thing special is that new/modified files will need to be copied locally from this special remote before being added to the annex (to get hash and such).
diff --git a/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_1_4d81941fe53881eebff97109a07ba2f4._comment b/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_1_4d81941fe53881eebff97109a07ba2f4._comment
new file mode 100644
index 000000000..1ec5bbc54
--- /dev/null
+++ b/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_1_4d81941fe53881eebff97109a07ba2f4._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="TroisSinges"
+ ip="82.227.207.5"
+ subject="comment 1"
+ date="2013-11-27T14:59:11Z"
+ content="""
+You could mount this NAS as a network drive on your computer (via samba for example or, even better, nfs), couldn't you? In this case you could use a real annex repository, and not a remote one.
+"""]]
diff --git a/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_2_660a5b764ad42468154b2bb94f8ec004._comment b/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_2_660a5b764ad42468154b2bb94f8ec004._comment
new file mode 100644
index 000000000..89663893e
--- /dev/null
+++ b/doc/forum/New_special_remote_suggeston_-_clean_directory/comment_2_660a5b764ad42468154b2bb94f8ec004._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://grossmeier.net/"
+ nickname="greg"
+ subject="mounting over NFS/etc ..."
+ date="2013-11-27T16:01:50Z"
+ content="""
+TroisSinges: Yeah, I could, but that'd limit me to being on the local network when I want to interact with the repo; not ideal.
+"""]]
diff --git a/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_1_6c74f0b43c457fe97b2d8630ca4fde29._comment b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_1_6c74f0b43c457fe97b2d8630ca4fde29._comment
new file mode 100644
index 000000000..8d2215772
--- /dev/null
+++ b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_1_6c74f0b43c457fe97b2d8630ca4fde29._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 1"
+ date="2013-11-08T18:24:27Z"
+ content="""
+The webapp sets up a dedicated ssh public key when you add a ssh repository in there.
+
+You might see some useful debugging info your your problem in ~/annex/.git/annex/daemon.log
+"""]]
diff --git a/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_2_b7a384e853e1756a684774348fad29e6._comment b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_2_b7a384e853e1756a684774348fad29e6._comment
new file mode 100644
index 000000000..ecf26daa1
--- /dev/null
+++ b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_2_b7a384e853e1756a684774348fad29e6._comment
@@ -0,0 +1,22 @@
+[[!comment format=mdwn
+ username="Auroch"
+ ip="87.65.174.80"
+ subject="OK,thanx for this"
+ date="2013-11-09T09:10:42Z"
+ content="""
+The problem is not solve, but with your informations, I think i've found somehting.
+
+Is it possible that the problem is linked to my situation of port-forwarding ?
+The remoteserver is a host (proxmox) with iptable port forwarding 62322 to the real port 22 of the VM hosting the git where I try to connect.
+
+So could the problem seems to be that some actions are taken on the host and not the VM ... correct ?
+
+    [2013-11-09 09:51:33 CET] read: ssh-keygen [\"-F\",\"bla.remote.tld\"]
+    [2013-11-09 09:51:33 CET] read: ssh [\"-oNumberOfPasswordPrompts=0\",\"-n\",\"-p\",\"62322\",\"user@bla.remote.tld\",\"sh -c 'echo git-annex-probe loggedin;if which git-annex-shell; then echo git-annex-probe git-annex-shell; fi;if which rsync; then echo git-annex-probe rsync; fi;if which ~/.ssh/git-annex-shell; then echo git-annex-probe ~/.ssh/git-annex-shell; fi'\"]
+    [2013-11-09 09:51:35 CET] chat: ssh [\"user@bla.remote.tld\",\"sh -c 'mkdir -p '\\"'\\"'annex'\\"'\\"'&&cd '\\"'\\"'annex'\\"'\\"'&&if [ ! -d .git ]; then git init --bare --shared; fi&&git annex init'\"]
+
+If it's correct, have you an idea for solving this ?
+
+best regards
+
+"""]]
diff --git a/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_3_3a8a7f51cb04a92c576549d379b57248._comment b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_3_3a8a7f51cb04a92c576549d379b57248._comment
new file mode 100644
index 000000000..546f647ed
--- /dev/null
+++ b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_3_3a8a7f51cb04a92c576549d379b57248._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 3"
+ date="2013-11-09T18:07:56Z"
+ content="""
+Well, it does look like your git-annex did not pass the port to the second command. 
+
+What version are you using? I've just tested with a ssh server only listening on 2222 and it used the port throughout.
+
+You might try upgrading to a recent version. I know that version 4.20130627, at least, had a bug with the ssh port.
+"""]]
diff --git a/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_4_582ad3ba0c62a77b08a10b37a780c670._comment b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_4_582ad3ba0c62a77b08a10b37a780c670._comment
new file mode 100644
index 000000000..c8d8c8b52
--- /dev/null
+++ b/doc/forum/Permission_denied___40__publickey__41___On_second_Step_...___63__/comment_4_582ad3ba0c62a77b08a10b37a780c670._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="Auroch"
+ ip="87.65.174.80"
+ subject="comment 4"
+ date="2013-11-09T19:24:54Z"
+ content="""
+I've the wheezy-backports version
+
+    i   4.20131002~bpo70+1                                                        wheezy-backports                                      100
+
+I'll have to wait an update and I'll come back to you.
+
+Thanx this amazing work !
+
+"""]]
diff --git a/doc/forum/Please_publish_new_releases_not_shorter_than_11_days.mdwn b/doc/forum/Please_publish_new_releases_not_shorter_than_11_days.mdwn
new file mode 100644
index 000000000..f67d2d797
--- /dev/null
+++ b/doc/forum/Please_publish_new_releases_not_shorter_than_11_days.mdwn
@@ -0,0 +1,6 @@
+Hi,
+i am following debian testing. The latest git-annex publication has manged to replace the former version on the last possible moment. Now another 10 days waiting.
+Would be nice if you can coordinate with testing.
+
+Thank you for git-annex. 
+Jürgen
diff --git a/doc/forum/Please_publish_new_releases_not_shorter_than_11_days/comment_1_da3d39de5be47ebe8b25a42ed1f36510._comment b/doc/forum/Please_publish_new_releases_not_shorter_than_11_days/comment_1_da3d39de5be47ebe8b25a42ed1f36510._comment
new file mode 100644
index 000000000..1fb259c98
--- /dev/null
+++ b/doc/forum/Please_publish_new_releases_not_shorter_than_11_days/comment_1_da3d39de5be47ebe8b25a42ed1f36510._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-03T19:57:24Z"
+ content="""
+I do coordinate with testing. That version had no possibility of ever reaching testing, since it failed to build on several architectures.
+"""]]
diff --git a/doc/forum/Purge_a_remote.txt b/doc/forum/Purge_a_remote.txt
new file mode 100644
index 000000000..f1b04ead2
--- /dev/null
+++ b/doc/forum/Purge_a_remote.txt
@@ -0,0 +1,2 @@
+How could I delete and purge a remote? I want to remove all traces of it
+but I can't find out how to achieve this.
diff --git a/doc/forum/Purge_a_remote/comment_1_78b3b77f457c65d31fd8a5abf714905d._comment b/doc/forum/Purge_a_remote/comment_1_78b3b77f457c65d31fd8a5abf714905d._comment
new file mode 100644
index 000000000..a7eff3a99
--- /dev/null
+++ b/doc/forum/Purge_a_remote/comment_1_78b3b77f457c65d31fd8a5abf714905d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-05T16:17:22Z"
+ content="""
+In the git-annex webapp, each repository has a settings menu with \"delete repository\".
+"""]]
diff --git a/doc/forum/Purge_a_remote/comment_2_dc65719157dee63b3979563ed57ee0ce._comment b/doc/forum/Purge_a_remote/comment_2_dc65719157dee63b3979563ed57ee0ce._comment
new file mode 100644
index 000000000..ddcab44dd
--- /dev/null
+++ b/doc/forum/Purge_a_remote/comment_2_dc65719157dee63b3979563ed57ee0ce._comment
@@ -0,0 +1,10 @@
+[[!comment format=txt
+ username="https://www.google.com/accounts/o8/id?id=AItOawkzwmw_zyMpZC9_J7ey--woeYPoZkAOgGw"
+ nickname="dxtrish"
+ subject="comment 2"
+ date="2013-11-05T17:46:02Z"
+ content="""
+When I use that Delete button it seems to still have records of it
+because when I delete the repo on the other end and create a new bare
+one it complains about some UUID mismatch.
+"""]]
diff --git a/doc/forum/Purge_a_remote/comment_3_63e0280273b816fa4b837724e102f813._comment b/doc/forum/Purge_a_remote/comment_3_63e0280273b816fa4b837724e102f813._comment
new file mode 100644
index 000000000..621bda508
--- /dev/null
+++ b/doc/forum/Purge_a_remote/comment_3_63e0280273b816fa4b837724e102f813._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-05T18:03:26Z"
+ content="""
+Hmm well, it's true that deleting a repository does not clean out any git remotes that other repositories might have configured using it, and the uuid of the old remote is cached in there. This is only a problem if you put back another repository in the same location as the old one. `git remote remove` should clean that up for you.
+"""]]
diff --git a/doc/forum/Purge_a_remote/comment_4_7fad1c4798ca03a4095ac3241c279f6d._comment b/doc/forum/Purge_a_remote/comment_4_7fad1c4798ca03a4095ac3241c279f6d._comment
new file mode 100644
index 000000000..afb4dc92e
--- /dev/null
+++ b/doc/forum/Purge_a_remote/comment_4_7fad1c4798ca03a4095ac3241c279f6d._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkzwmw_zyMpZC9_J7ey--woeYPoZkAOgGw"
+ nickname="dxtrish"
+ subject="comment 4"
+ date="2013-11-06T14:24:21Z"
+ content="""
+That is exactly what I have wanted to do a couple of times now and 'git remote remove' does not seem to remove it all either.
+When I try to create a new repository in the same place it still complains about that darn UUID :)
+
+What is working is to manually add the new UUID to .git/config
+"""]]
diff --git a/doc/forum/Retrieve_previous_version_in_direct_mode/comment_2_1292b34ff6d9976b2bd08748e1ba4e7a._comment b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_2_1292b34ff6d9976b2bd08748e1ba4e7a._comment
new file mode 100644
index 000000000..47ab2b742
--- /dev/null
+++ b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_2_1292b34ff6d9976b2bd08748e1ba4e7a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="Disk space?"
+ date="2013-11-02T01:33:10Z"
+ content="""
+Sorry, I'm confused: does using regular client repositories in direct mode still store old versions of files?  If so, for how long?  I don't have unlimited disk space, and if it stored in git every copy of every file forever, especially large ones, I'd run out of space...and then what?
+"""]]
diff --git a/doc/forum/Retrieve_previous_version_in_direct_mode/comment_3_699e816c0397f6db924feeab906f1151._comment b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_3_699e816c0397f6db924feeab906f1151._comment
new file mode 100644
index 000000000..77fa9b0e7
--- /dev/null
+++ b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_3_699e816c0397f6db924feeab906f1151._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T17:36:23Z"
+ content="""
+You can use `git annex unused` and `git annex dropunused` to remove old versions of files.
+"""]]
diff --git a/doc/forum/Retrieve_previous_version_in_direct_mode/comment_4_d900388753de5870b7b9c0e8b8c06ed7._comment b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_4_d900388753de5870b7b9c0e8b8c06ed7._comment
new file mode 100644
index 000000000..deb26163e
--- /dev/null
+++ b/doc/forum/Retrieve_previous_version_in_direct_mode/comment_4_d900388753de5870b7b9c0e8b8c06ed7._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 4"
+ date="2013-11-02T22:30:07Z"
+ content="""
+Thank you.  Just curious, are there plans to put that in the webapp?
+"""]]
diff --git a/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_10_bcb883d46a637dd1a8ef9a92733d202a._comment b/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_10_bcb883d46a637dd1a8ef9a92733d202a._comment
new file mode 100644
index 000000000..5064de49d
--- /dev/null
+++ b/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_10_bcb883d46a637dd1a8ef9a92733d202a._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 10"
+ date="2013-11-08T18:32:12Z"
+ content="""
+If I could comprehensively fix that bug I would.
+
+But, it's supposed to already be fixed when using direct mode. Were you using indirect mode when you saw the problem?
+"""]]
diff --git a/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_11_b7a8b9eaf114f883866fbf2be51b622f._comment b/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_11_b7a8b9eaf114f883866fbf2be51b622f._comment
new file mode 100644
index 000000000..7155b560f
--- /dev/null
+++ b/doc/forum/Slightly_finer_control_over_file_whereabouts/comment_11_b7a8b9eaf114f883866fbf2be51b622f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnSenxKyE_2Z6Wb-EBMO8FciyRywjx1ZiQ"
+ nickname="Walter"
+ subject="comment 11"
+ date="2013-11-09T06:02:36Z"
+ content="""
+No, this was using direct mode.
+"""]]
diff --git a/doc/forum/Some_mounted_devices_not_detected.mdwn b/doc/forum/Some_mounted_devices_not_detected.mdwn
new file mode 100644
index 000000000..6146ef14f
--- /dev/null
+++ b/doc/forum/Some_mounted_devices_not_detected.mdwn
@@ -0,0 +1,3 @@
+Automounted USB devices are not detected by the git-annex webapp on my Debian testing/squeeze installation, only drives with entries in /etc/fstab show up in the device list. Is there any way to tweak/get around this?
+
+I'm running version 4.20131106 (couldn't manage to build the package for sid). 
diff --git a/doc/forum/Some_mounted_devices_not_detected/comment_1_0ba07b95f12f57ea63bb450b88430c45._comment b/doc/forum/Some_mounted_devices_not_detected/comment_1_0ba07b95f12f57ea63bb450b88430c45._comment
new file mode 100644
index 000000000..5cd472c8e
--- /dev/null
+++ b/doc/forum/Some_mounted_devices_not_detected/comment_1_0ba07b95f12f57ea63bb450b88430c45._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-24T16:04:23Z"
+ content="""
+can you post an example line from /proc/mounts for one of these devices?
+"""]]
diff --git a/doc/forum/Some_mounted_devices_not_detected/comment_2_4f8c7bcd0f20dafa5635a3580ec8d1f6._comment b/doc/forum/Some_mounted_devices_not_detected/comment_2_4f8c7bcd0f20dafa5635a3580ec8d1f6._comment
new file mode 100644
index 000000000..60512d418
--- /dev/null
+++ b/doc/forum/Some_mounted_devices_not_detected/comment_2_4f8c7bcd0f20dafa5635a3580ec8d1f6._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmyEv6SesaYeke389mHdiHlavirPkGHzHI"
+ nickname="Albin"
+ subject="comment 2"
+ date="2013-11-26T14:35:58Z"
+ content="""
+I missed your reply on IRC. Sorry for that!
+
+Here's an example from /proc/mounts:
+
+   /dev/sdf1 /media/SoderUSB ext4 rw,nosuid,nodev,noexec,relatime,errors=remount-ro,data=ordered 0 0
+
+"""]]
diff --git a/doc/forum/Some_mounted_devices_not_detected/comment_3_06c0db7d670d9b82823102d22db15a36._comment b/doc/forum/Some_mounted_devices_not_detected/comment_3_06c0db7d670d9b82823102d22db15a36._comment
new file mode 100644
index 000000000..53c76e210
--- /dev/null
+++ b/doc/forum/Some_mounted_devices_not_detected/comment_3_06c0db7d670d9b82823102d22db15a36._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 3"
+ date="2013-11-26T19:59:42Z"
+ content="""
+Hmm, that looks fine.
+
+Perhaps the user you're running git-annex as cannot write to `/media/SoderUSB` ? The webapp avoids listing places you can't write, since it would fail to make a repository there. (Also because this is an easy way for it to avoid listing `/`, `/usr`, or whatever other OS-level mounts a system might have..)
+"""]]
diff --git a/doc/forum/Some_mounted_devices_not_detected/comment_4_80820a29361c5be4a94672dacfdefa6f._comment b/doc/forum/Some_mounted_devices_not_detected/comment_4_80820a29361c5be4a94672dacfdefa6f._comment
new file mode 100644
index 000000000..03b917a69
--- /dev/null
+++ b/doc/forum/Some_mounted_devices_not_detected/comment_4_80820a29361c5be4a94672dacfdefa6f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmyEv6SesaYeke389mHdiHlavirPkGHzHI"
+ nickname="Albin"
+ subject="comment 4"
+ date="2013-11-27T17:33:22Z"
+ content="""
+Actually, that (write permissions) seems to have been the problem. Thanks! Can't imagine why pmount would not mount a device writable by my user, though.
+"""]]
diff --git a/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version.mdwn b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version.mdwn
new file mode 100644
index 000000000..1f8730514
--- /dev/null
+++ b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version.mdwn
@@ -0,0 +1,9 @@
+Hi!
+
+Just tried various android ssh servers which do work, but have no access to the command line tools shipped with git annex.
+
+From what I gather from the planning docs, sshd was stripped from the android tools to save space. If this were the case, it (naively) seems to me it would have to be simple to re-enable.
+
+Rationale: It would make it super convenient to use command line git annex on my phone alongside the assistant, through letting me type on my desktop. Not to mention that the command line tools shipped with git annex are by far the best around for android work.
+
+Carlo
diff --git a/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_1_5c2f376a82458c6387560355940419d3._comment b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_1_5c2f376a82458c6387560355940419d3._comment
new file mode 100644
index 000000000..9a39a2e4c
--- /dev/null
+++ b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_1_5c2f376a82458c6387560355940419d3._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-02T19:42:13Z"
+ content="""
+sshd was removed from the bundle because it's not needed for git-annex to be used on Android, and it would be very complicated to get it to work. (And would require rooting the device at least for port 22 and probably also since sshd needs to run as root generally.)
+
+If there are android ssh servers that let you choose which user to log in as, you could log in as the app_NN user corresponding to the git-annex android app, and have all the tools available, once you ran runshell. I belive there's also an equivilant to su on android that lets you change to an app_NN user, although you probably already need root.
+
+I think it's more usual to use adb in these situations.
+"""]]
diff --git a/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_2_6321dec0b2f22f841f3cb986e063113f._comment b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_2_6321dec0b2f22f841f3cb986e063113f._comment
new file mode 100644
index 000000000..b1ce5a1a5
--- /dev/null
+++ b/doc/forum/Suggestion:_Put_ssh_server_back_into_android_version/comment_2_6321dec0b2f22f841f3cb986e063113f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnZEanlyzay_QlEAL0CWpyZcRTyN7vay8U"
+ nickname="Carlo"
+ subject="comment 2"
+ date="2013-11-03T09:48:53Z"
+ content="""
+Ah, the \"very complicated to get it to work\" part is what I didn't know, thanks for explaining and or the tips.
+"""]]
diff --git a/doc/forum/Syncronisation_of_syncronisation_between_3_repositories__63__/comment_1_ca5192a26950627a1c2efcb55d6d2fa3._comment b/doc/forum/Syncronisation_of_syncronisation_between_3_repositories__63__/comment_1_ca5192a26950627a1c2efcb55d6d2fa3._comment
index 2cc0c9296..dccd1d8d5 100644
--- a/doc/forum/Syncronisation_of_syncronisation_between_3_repositories__63__/comment_1_ca5192a26950627a1c2efcb55d6d2fa3._comment
+++ b/doc/forum/Syncronisation_of_syncronisation_between_3_repositories__63__/comment_1_ca5192a26950627a1c2efcb55d6d2fa3._comment
@@ -6,5 +6,5 @@
  content="""
 git-annex does not currently prevent multiple uploads of the same file to a rsync special remote. It is able to guard against this when uploading to a git remote, since then the remote runs git-annex-shell, which can detect when an upload is already running. You might want to convert your rsync remote to a git remote.
 
-I hope that rsyncing the same file twice at the same time is safe, but it's certianly excessively expensive.
+I hope that rsyncing the same file twice at the same time is safe, but it's certainly excessively expensive.
 """]]
diff --git a/doc/forum/Two_computer_setup:___34__transfer__34___or___34__full_backup__34___repository_groups__63__/comment_2_50cafde7e30b928480d1f142ddd763d2._comment b/doc/forum/Two_computer_setup:___34__transfer__34___or___34__full_backup__34___repository_groups__63__/comment_2_50cafde7e30b928480d1f142ddd763d2._comment
new file mode 100644
index 000000000..4495401b2
--- /dev/null
+++ b/doc/forum/Two_computer_setup:___34__transfer__34___or___34__full_backup__34___repository_groups__63__/comment_2_50cafde7e30b928480d1f142ddd763d2._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 2"
+ date="2013-11-01T16:47:18Z"
+ content="""
+git-annex keeps track of the repository group on a per repository basis. That is, if the repository on Server-A is a full backup, both Client-A and Client-B will consider it to be one, and use it appropriately. You can't have just Client-A think it's a full backup; this setting will be automatically synced to Client-B.
+
+Your setup sounds ok, although you might need to set up a XMPP account in order for Client-A and Client-B to immediately message one-another when they have new changes to sync. Otherwise, they might only poll Server-A occasionally for changes.
+"""]]
diff --git a/doc/forum/USB_backup_with_files_visible/comment_6_add048a16837f7940a859f21426cdbe9._comment b/doc/forum/USB_backup_with_files_visible/comment_6_add048a16837f7940a859f21426cdbe9._comment
new file mode 100644
index 000000000..95f749574
--- /dev/null
+++ b/doc/forum/USB_backup_with_files_visible/comment_6_add048a16837f7940a859f21426cdbe9._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="Confused"
+ date="2013-11-03T00:13:47Z"
+ content="""
+Sorry, I'm confused.  I set up a Full Backup repo on a second hard drive, but the files are visible in its directory just like in my Client repos' directories.  Are the files not supposed to be visible?  Is something wrong?
+"""]]
diff --git a/doc/forum/USB_backup_with_files_visible/comment_7_de227ca9911fe57d7a6d3e037f574fe9._comment b/doc/forum/USB_backup_with_files_visible/comment_7_de227ca9911fe57d7a6d3e037f574fe9._comment
new file mode 100644
index 000000000..0f74efac0
--- /dev/null
+++ b/doc/forum/USB_backup_with_files_visible/comment_7_de227ca9911fe57d7a6d3e037f574fe9._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 7"
+ date="2013-11-03T01:09:16Z"
+ content="""
+You can set it up that way, but the often confusing behavior (including not being able to umount a drive that has the git-annex assistant deamon running in it!) is why the webapp attempt to steer users toward making bare reposotories on USB drives.
+
+If you click on \"Add another repository\" -> \"Removable drive\", you get a bare repository.
+
+If you click on upper-right menu -> \"Add another local repository\" and enter a path, and tell it to combine the repositories, you get a synced non-bare repository, and potentially problems unmounting the drive since you now have 2 assistant daemons running.
+
+I have now added a further link to the nice removable drive path to that second UI path.
+"""]]
diff --git a/doc/forum/USB_backup_with_files_visible/comment_8_0c0ed0e038f7f0e2d2d4ed69b7b29fbc._comment b/doc/forum/USB_backup_with_files_visible/comment_8_0c0ed0e038f7f0e2d2d4ed69b7b29fbc._comment
new file mode 100644
index 000000000..6511343e8
--- /dev/null
+++ b/doc/forum/USB_backup_with_files_visible/comment_8_0c0ed0e038f7f0e2d2d4ed69b7b29fbc._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 8"
+ date="2013-11-03T01:13:26Z"
+ content="""
+Thanks for the explanation, Joey.  I just posted a [comment](http://git-annex.branchable.com/bugs/Unnecessary_remote_transfers/#comment-f7110e694a9951d8ab546b8dec568bfa) about this on the bug report too.  Maybe the problem is simply that the Removable Drive option doesn't allow using internal, non-removable drives.
+
+BTW, I don't know if this is relevant, but I only see one \"git-annex assistant\" process running.
+"""]]
diff --git a/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__.mdwn b/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__.mdwn
new file mode 100644
index 000000000..985bff87c
--- /dev/null
+++ b/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__.mdwn
@@ -0,0 +1,36 @@
+I don't know if this is an "unusual setup" or something that should be supported, but it seems like a reasonable use case to me, so here goes:
+
+I have three systems: a desktop, a laptop, and a little netbook.  I have one main annex that is currently synced between the desktop and the laptop at ~/annex on both, and to a secondary, Full Backup repo on the desktop, under /mnt.
+
+I have some music on my laptop, and I like to sync ~/Music between the laptop and the netbook.  So I thought I'd make a new git-annex repo at ~/Music on both and sync them.  I want this to be kept separate from ~/annex.
+
+I also thought it would be good to backup the music, so I thought I'd connect laptop:~/Music to the Full Backup repo at desktop:/mnt.  So I paired the repo at laptop:~/Music to the repo at desktop:/mnt.
+
+So I had set up these repos:
+
+* desktop:
+  * /mnt  (Full Backup)
+  * ~/annex  (Client)
+* laptop:
+  * ~/annex  (Client)
+  * ~/Music  (Client)
+* netbook:
+  * ~/Music  (Client)
+
+As I feared--but I wasn't sure, since I'm new to git-annex--since the desktop:/mnt repo was connected to laptop:~/Music, and desktop:~/mnt was also connected to desktop:~/annex,  this caused everything in laptop:~/Music to be synced to desktop:~/annex, because they were part of the same "set" of repos; they were all in the same .git/config files.
+
+So now I have a few problems:
+
+1.  How do I get all these music files out of my ~/annex repos?  I tried removing the remote repos from ~/annex/.git/config and then running 'git-annex unused', but that didn't result in it thinking all the music files were unused.  Do I have to delete them all manually?  (There are a *lot* of directories from ~/Music now in ~/annex).
+
+2.  It seems that desktop:~/annex/.git is...now over 600 MB, even though few of the actual music files have synced over.  Is it possible to clean out ~/annex/.git and restore it to the pre-mess state without starting from scratch?
+
+3.  Is it possible--or reasonable--to use a single Full Backup repo for multiple independent client repos?  That is, is it possible to do that without the independent client repos "cross-pollinating"?  Or do I need to use separate Full Backup repos for each "set" of client repos?
+
+4.  I'm not sure if this is a separate problem, but I just want to make sure I understand the best way to handle things like this.  I wanted to disconnect desktop:~/annex from laptop:~/Music, but I thought that if I used the webapp to "Delete" the laptop:~/Music repo, it would actually start deleting the music files in laptop:~/Music, after moving them to desktop:~/annex.  Am I correct that that would have happened?  If so, "Deleting" a repo seems like a dangerous operation that should warn and prompt the user.  Maybe an "unlink repo" option needs to be available to simply disconnect two repos and leave their respective contents intact.
+
+I apologize if these are newbie problems.  Despite reading every dev blog entry--both before and after the switchover--I'm still new to actually using git-annex.  I'm not sure if it's supposed to work this way or if I'm using it wrong.
+
+If I am using it wrong...well, I can imagine other git-annex newbies doing similar things and ending up with similar messes, so maybe this needs to...be considered or something.  :)  Since I'm still experimenting with git-annex, I haven't put any "live" data in it, so I can blow away all the annexes and start over, but I would like to learn how to properly fix a situation like this in case I goof up in the future.
+
+Thanks for your help.
diff --git a/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__/comment_1_c61c28600f1079fb03ddabc950307f27._comment b/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__/comment_1_c61c28600f1079fb03ddabc950307f27._comment
new file mode 100644
index 000000000..b7119aa2d
--- /dev/null
+++ b/doc/forum/Using_a_single_backup_repo_for_multiple_independent_client_repos__63__/comment_1_c61c28600f1079fb03ddabc950307f27._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-05T16:14:34Z"
+ content="""
+1. Turn off the assistant, switch to indirect mode (`git annex indirect`), use `git log --stat` to find the commit(s) that added the music files, and `git revert` the commits, in reverse chronological order. Or delete the files manually.
+2. You have merged two git repositories. Without some serious git repository surgery (ie, resetting to an old version and deleting the reflog), the full history of both is going to remain stored in git going forward. However, a simple `git gc` might pack that down to a much smaller amount of disk space.
+3. Combining two repositories merges their git histories. You then have two clones of one repository containing the full contents and git history of both. Don't do that if that's not what you want. The webapp is always careful to tell you when an action will combine two repositories.
+4. Once you have combined two repositories, you have two synced repositories that contain the same data. Deleting one of them will just delete one copy of the data. It won't result in data loss, but neither will it untangle the two git trees that were previously combined.
+"""]]
diff --git a/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_3_076f22d05fad140068a540e4d835106f._comment b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_3_076f22d05fad140068a540e4d835106f._comment
new file mode 100644
index 000000000..0fb4f61e2
--- /dev/null
+++ b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_3_076f22d05fad140068a540e4d835106f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-01T16:42:33Z"
+ content="""
+Files in the git repository whose content has not yet been downloaded will appear as these short placeholder files when using a filesystem that does not support symlinks. Once the files have been downloaded, that is replaced with their actual content. You may need to set up a way to your android tablet to download the files from the place they're being created.
+"""]]
diff --git a/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_4_c8446ee1b817f1824fa0df07e742015c._comment b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_4_c8446ee1b817f1824fa0df07e742015c._comment
new file mode 100644
index 000000000..cd42b6c15
--- /dev/null
+++ b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_4_c8446ee1b817f1824fa0df07e742015c._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="Mebus"
+ ip="2001:4dd0:ff00:29::2"
+ subject="comment 4"
+ date="2013-11-11T20:24:11Z"
+ content="""
+Does it have to be the place, where they were created or can this also be a central server, I pushed everything to?
+
+Mebus
+
+
+"""]]
diff --git a/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_5_f746c1b85ee8e4b57b6819ccceabd28b._comment b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_5_f746c1b85ee8e4b57b6819ccceabd28b._comment
new file mode 100644
index 000000000..676e7b6f1
--- /dev/null
+++ b/doc/forum/Using_git_annex_with_Android_tablet_which_only_has_exFAT_and_no_symlinks/comment_5_f746c1b85ee8e4b57b6819ccceabd28b._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 5"
+ date="2013-11-13T16:37:46Z"
+ content="""
+The git-annex app will download the files from any remote you set up that has a copy of the file. A transfer remote in the cloud would work well.
+"""]]
diff --git a/doc/forum/XBMC__44___NFS___38___git-annex_/comment_2_d8ed4dd51d3050db691a8abdec24cd42._comment b/doc/forum/XBMC__44___NFS___38___git-annex_/comment_2_d8ed4dd51d3050db691a8abdec24cd42._comment
index d2330e336..0b3cb22c1 100644
--- a/doc/forum/XBMC__44___NFS___38___git-annex_/comment_2_d8ed4dd51d3050db691a8abdec24cd42._comment
+++ b/doc/forum/XBMC__44___NFS___38___git-annex_/comment_2_d8ed4dd51d3050db691a8abdec24cd42._comment
@@ -6,5 +6,5 @@
  content="""
 The default git-annex backend for over a year now is SHA256E, which includes the filename extension in the key to deal with programs that rely on them. If you're not using that backend, you can `git annex migrate` to it.
 
-Or you can turn on direct mode, which will certianly solve the problem.
+Or you can turn on direct mode, which will certainly solve the problem.
 """]]
diff --git a/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__.mdwn b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__.mdwn
new file mode 100644
index 000000000..a9db915da
--- /dev/null
+++ b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__.mdwn
@@ -0,0 +1,45 @@
+Hi,
+
+Some time ago I asked [[here|git_annex_copy_--fast_--to_blah_much_slower_than_--from_blah]]
+about possible improvements in git `copy --fast --to`, since it was painfully slow
+on moderately large repos.
+
+Now I found a way to make it much faster for my particular use case, by
+accessing some annex internals. And I realized that maybe commands like `git
+annex find --in=repo` do not batch queries to the location log. This is based on
+the following timings, on a new repo (only a few commits) and about 30k files.
+
+    > time git annex find --in=skynet > /dev/null
+
+    real	0m55.838s
+    user	0m30.000s
+    sys	0m1.583s
+
+
+    > time git ls-tree -r git-annex | cut -d ' ' -f 3 | cut -f 1 | git cat-file --batch > /dev/null
+
+    real	0m0.334s
+    user	0m0.517s
+    sys	0m0.030s
+
+Those numbers are on linux (with an already warm file cache) and an ext4 filesystem on a SSD.
+
+The second command above is feeding a list of objects to a single `git cat-file`
+process that cats them all to stdout, preceeding every file dump by the object
+being cat-ed. It is a trivial matter to parse this output and use it for
+whatever annex needs.
+
+Above I wrote a `git ls-tree` on the git-annex branch for simplicity, but we could
+just as well do a `ls-tree | ... | git cat-file` on HEAD to get the keys for the
+annexed files matching some path and then feed those keys to a cat-file on
+the git-annex branch. And this still would be an order of magnitude faster than
+what currently annex seems to do.
+
+I'm assuming the bottleneck is in that annex does not batch the `cat-file`, as the rest of logic needed for a find will be fast. Is that right? 
+
+Now, if the queries to the location log for `copy --to` and `find` could be batched this way, the
+performance of several useful things to do, like checking how many annexed files
+we are missing, would be bastly improved. Hell, I could even put that number on
+the command line prompt!
+
+I'm not yet very fluent in Haskell, but I'm willing to help if this is something that makes sense and can be done.
diff --git a/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_1_01cbfc513c790faef3a3ede5315d3589._comment b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_1_01cbfc513c790faef3a3ede5315d3589._comment
new file mode 100644
index 000000000..6b4a6b2a0
--- /dev/null
+++ b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_1_01cbfc513c790faef3a3ede5315d3589._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-06T22:21:33Z"
+ content="""
+git-annex uses cat-file --batch, yes. You can verify this with --debug. Or you can read Annex/CatFile.hs and Git/CatFile.hs
+
+git-annex has to ensure that the git-annex branch is up-to-date and that any info synced into the repository is merged into it. This can require several calls to git log. Your command does not do that. git-annex find also runs `git ls-files --cached`, which has to examine the state of the index and of files on disk, in order to only show files that are in the working tree. Your command also omits that.
+"""]]
diff --git a/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_2_fe28dfb360caa12d5d5bc186def3eb45._comment b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_2_fe28dfb360caa12d5d5bc186def3eb45._comment
new file mode 100644
index 000000000..4ba4c8264
--- /dev/null
+++ b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_2_fe28dfb360caa12d5d5bc186def3eb45._comment
@@ -0,0 +1,35 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkkyBDsfOB7JZvPZ4a8F3rwv0wk6Nb9n48"
+ nickname="Abdó"
+ subject="comment 2"
+ date="2013-11-06T23:14:03Z"
+ content="""
+Ok, then I don't understand where annex spends its time. git annex takes 55
+seconds! vs less than a second for a batched query on all the keys in the
+location log. Checking that branches are in sync, or traversing the working dir
+shouldn't amount the extra 54 seconds! At least not on a recently synced repo
+with up to date index and clean working dir.
+
+> git-annex has to ensure that the git-annex branch is up-to-date and that any info synced into the repository is merged into it. This can require several calls to git log
+
+Ok, I understand that. Checking that should be typically fast though, isn't it? On a repo that has just been synced, it doesn't need to go very far on the log.
+
+> git-annex find also runs git ls-files --cached, which has to examine the state of the index and of files on disk, in order to only show files that are in the working tree
+
+I understand that too. For my particular use case, I know I do the `git copy` when the
+repo is in sync and the working dir has no uncommited changes. So I use HEAD to retrieve the keys for
+the files in the working tree. I do something like that:
+
+    time git ls-tree -r HEAD | grep -e '^120000' | cut -d ' ' -f 3 | cut -f 1 | git cat-file --batch > /dev/null
+
+    real	0m0.178s
+    user	0m0.277s
+    sys 	0m0.037s
+
+That plus some fast parsing of the output gets the list of keys for the files in HEAD in less than a second. Where do the 54 extra seconds hide, then?
+
+Mm... how does annex retrieve the keys for files in the working tree? Does it follow
+the actual symlinks on the filesystem? I can believe that following 30k symlinks may be slow (although not 55 second slow).
+
+Sorry for being so insistent on this... It is just that I do think the same can be done much faster, and such an improvement in performance would be very interesting, not only for me.
+"""]]
diff --git a/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_3_9bb30ab62febe4ef63bed49f831a473a._comment b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_3_9bb30ab62febe4ef63bed49f831a473a._comment
new file mode 100644
index 000000000..c92be8ad5
--- /dev/null
+++ b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_3_9bb30ab62febe4ef63bed49f831a473a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-07T18:12:09Z"
+ content="""
+It's hard to say until some profiling has actually been done. Comparing apples and oranges, or perhaps better to say, orange blossoms and oranges, is not very useful. 
+"""]]
diff --git a/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_4_7832f0347a41b8204538c01b72487803._comment b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_4_7832f0347a41b8204538c01b72487803._comment
new file mode 100644
index 000000000..3e7eb01db
--- /dev/null
+++ b/doc/forum/_Does_git_annex_find___40____38___friends__41___batch_queries_to_the_location_log__63__/comment_4_7832f0347a41b8204538c01b72487803._comment
@@ -0,0 +1,19 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkkyBDsfOB7JZvPZ4a8F3rwv0wk6Nb9n48"
+ nickname="Abdó"
+ subject="comment 4"
+ date="2013-11-07T18:40:27Z"
+ content="""
+Ok, thanks.
+
+I understand that annex is more sophisticated than what I'm proposing. I'm also
+not comparing apples to oranges, what I'm saying is this: All the
+logic and checking and git calls that I thought annex needs to do, take
+much much less time than those 55 seconds. So either I'm missing something big (about 98% of it in execution time), or
+annex is doing something very inefficient. That's all I'm saying, and I was
+hoping that you could clarify that, since you already know the code.
+
+Also I'm sorry for being so annoying. If annex were writen in C, I would either have understood those 55 seconds or sent you a patch making annex faster. Being in
+haskell means that it will take me considerably more time and effort. But if I manage to
+improve things and if it is ok with you I'll send you patches... eventually.
+"""]]
diff --git a/doc/forum/_preferred_content:_lastpresent.mdwn b/doc/forum/_preferred_content:_lastpresent.mdwn
new file mode 100644
index 000000000..e8730eb00
--- /dev/null
+++ b/doc/forum/_preferred_content:_lastpresent.mdwn
@@ -0,0 +1 @@
+Is there any kind of "lastpresent" in the preferred-content expression? If set, git-annex would see if "git log --follow $path -n 1" (or some configurable -n) was present.
diff --git a/doc/forum/_preferred_content:_lastpresent/comment_1_7610cd866b256d36646b642eb5f8cae5._comment b/doc/forum/_preferred_content:_lastpresent/comment_1_7610cd866b256d36646b642eb5f8cae5._comment
new file mode 100644
index 000000000..d5910c6d0
--- /dev/null
+++ b/doc/forum/_preferred_content:_lastpresent/comment_1_7610cd866b256d36646b642eb5f8cae5._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-15T20:39:43Z"
+ content="""
+The idea seems to be to match files that have been deleted.
+
+I don't see how that could work; preferred content expressions are always matched against files in the working tree.
+
+Even if it were doable, it would be quite expensive if every preferred content query involved a `git log`...
+
+What are you trying to achieve with this?
+"""]]
diff --git a/doc/forum/_preferred_content:_lastpresent/comment_2_d25666a173b78213d583f029fd166d06._comment b/doc/forum/_preferred_content:_lastpresent/comment_2_d25666a173b78213d583f029fd166d06._comment
new file mode 100644
index 000000000..4714034c3
--- /dev/null
+++ b/doc/forum/_preferred_content:_lastpresent/comment_2_d25666a173b78213d583f029fd166d06._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawn1QhtPvsRBV7pfaDW_ZTPFv_ZIxSzQ8Rg"
+ nickname="Paul Léo"
+ subject="comment 2"
+ date="2013-11-16T13:12:35Z"
+ content="""
+The aim is to be able to have some semi-automatic mode (using \"git-annex wanted . (lastpresent)\"), where file paths which you \"git-annex get\" one time always get updated to the latest version.
+
+Or, you could also use some variant of it the other way round (using \"git-annex wanted . (notlastpresent)\"): all files would be present by default, but paths which you \"git-annex drop\"ed once wouldn't become present again.
+"""]]
diff --git a/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__.mdwn b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__.mdwn
new file mode 100644
index 000000000..e48bf4cf6
--- /dev/null
+++ b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__.mdwn
@@ -0,0 +1,10 @@
+Hi,
+
+I am trying to understand git-annex, and the walkthroughs on the page did help a lot. I *feel* that git-annex is the solution for my use case: having a large archive, several computers, NAS both at work and at home, being offline during commuting, …
+
+Everything seems to be clear for me when using the command line version. Using annex assistant looks promising, and it is easy to create repositories that match my usage. But now I see that these repositories are in direct mode by default; and I am not sure how this impacts my ability to work with large files. I do not want to end up with git (without annex) handling huge files.
+
+So - can somebody explain how direct mode affects this? Can I switch to indirect mode with the assistant? Am I asking the wrong questions? 
+
+thanks,
+Ulli
diff --git a/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_1_d90d1d599ce557af03c6f0f2ea188212._comment b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_1_d90d1d599ce557af03c6f0f2ea188212._comment
new file mode 100644
index 000000000..d762791da
--- /dev/null
+++ b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_1_d90d1d599ce557af03c6f0f2ea188212._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-09T17:36:01Z"
+ content="""
+Files in direct mode are stored in the git annex the same way as when using indirect mode. But you're perhaps right to be wary of using direct mode, it's been quite easy to mess up while using it at the command line until very recently when the [[todo/direct_mode_guard]] was implemented.
+
+You can switch repositories created using the assistant from direct to indirect mode if you like. The assistant works in either mode.
+"""]]
diff --git a/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_2_58b1af497cab132acb28cb5f9283ec2a._comment b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_2_58b1af497cab132acb28cb5f9283ec2a._comment
new file mode 100644
index 000000000..45cec4db5
--- /dev/null
+++ b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_2_58b1af497cab132acb28cb5f9283ec2a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="Thanks"
+ date="2013-11-12T08:57:36Z"
+ content="""
+Ok, thanks for the explanation. I still have to figure out what happens when I annex drop files on a direct repository, and how well all this plays with the Finder on Mac…
+"""]]
diff --git a/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_3_37d4fd8f69e8066b5aa19454b714e443._comment b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_3_37d4fd8f69e8066b5aa19454b714e443._comment
new file mode 100644
index 000000000..71a091930
--- /dev/null
+++ b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_3_37d4fd8f69e8066b5aa19454b714e443._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="So what does &quot;git annex drop&quot; do in direct mode?"
+ date="2013-11-15T15:07:57Z"
+ content="""
+I just tried a git annex drop on a file in a direct mode repository, and that just did not change anything at all, as far as I can see. Actually I don't know what to expect, but doesn't that mean that I should have to switch to indirect mode in order to be able to drop large files to save space? 
+
+Funny is that git annex drop did not complain at all but just reported \"ok\" after quite a while. And when I tried to drop a file that was not available in any other repository, it failed (which is expected behavior). So what is it what was \"ok\"?
+
+"""]]
diff --git a/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_4_a974e2105774d4f82ad286ff0792ba84._comment b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_4_a974e2105774d4f82ad286ff0792ba84._comment
new file mode 100644
index 000000000..587d704d3
--- /dev/null
+++ b/doc/forum/assistant__44___direct_mode__44___large_files__44___command_line_-_how_do_these_play_together__63__/comment_4_a974e2105774d4f82ad286ff0792ba84._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 4"
+ date="2013-11-15T20:33:47Z"
+ content="""
+Drop in direct mode does the same thing as in indirect mode.
+
+If you are using git-annex on a crippled filesystem without symlinks, git-annex cannot represent a file whose content has been dropped using a broken symlink, so it instead represents it with a nearly empty file.
+"""]]
diff --git a/doc/forum/assistant_created_encrypted__backup_remote:_Howto_restore__63__/comment_2_173da510b45f0320ae8aa2df9f14ae7b._comment b/doc/forum/assistant_created_encrypted__backup_remote:_Howto_restore__63__/comment_2_173da510b45f0320ae8aa2df9f14ae7b._comment
new file mode 100644
index 000000000..dbf2178f5
--- /dev/null
+++ b/doc/forum/assistant_created_encrypted__backup_remote:_Howto_restore__63__/comment_2_173da510b45f0320ae8aa2df9f14ae7b._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="Frank"
+ ip="31.19.114.93"
+ subject="Comment 2"
+ date="2013-11-07T19:45:16Z"
+ content="""
+Thank you very much for the explanation! Have fun!
+
+
+
+"""]]
diff --git a/doc/forum/could_not_read_from_remote_repository.mdwn b/doc/forum/could_not_read_from_remote_repository.mdwn
new file mode 100644
index 000000000..6103bfd36
--- /dev/null
+++ b/doc/forum/could_not_read_from_remote_repository.mdwn
@@ -0,0 +1,36 @@
+hi, i'm trying to set up my notebook and desktop pc to sync my documents. so i used local computers in the web app as a sync option, but on my notebook i get the following error:
+
+    [2013-11-26 11:29:03 CET] main: Pairing in progress
+    X11 forwarding request failed
+    /home/max/.ssh/git-annex-shell: line 4: exec: git-annex-shell: not found
+    X11 forwarding request failed on channel 0
+    /home/max/.ssh/git-annex-shell: line 4: exec: git-annex-shell: not found
+    fatal: Could not read from remote repository.
+    
+    Please make sure you have the correct access rights
+    and the repository exists.
+    [2013-11-26 11:29:31 CET] PairListener: Syncing with desk_Private_Dokumente 
+    X11 forwarding request failed on channel 0
+    /home/max/.ssh/git-annex-shell: line 4: exec: git-annex-shell: not found
+    fatal: Could not read from remote repository.
+
+    Please make sure you have the correct access rights
+    and the repository exists.
+
+    merge: refs/remotes/desk_Private_Dokumente/master - not something we can merge
+
+    merge: refs/remotes/desk_Private_Dokumente/synced/master - not something we can merge
+    X11 forwarding request failed
+    /home/max/.ssh/git-annex-shell: line 4: exec: git-annex-shell: not found
+    X11 forwarding request failed on channel 0
+    /home/max/.ssh/git-annex-shell: line 4: exec: git-annex-shell: not found
+    fatal: Could not read from remote repository.
+
+    Please make sure you have the correct access rights
+    and the repository exists.
+
+my desktop succeeded in adding the repository. 
+
+any idea whats going wrong ?
+
+thanks
diff --git a/doc/forum/could_not_read_from_remote_repository/comment_1_27d4d1556a80c06505ed3d8a9422d082._comment b/doc/forum/could_not_read_from_remote_repository/comment_1_27d4d1556a80c06505ed3d8a9422d082._comment
new file mode 100644
index 000000000..aaf094693
--- /dev/null
+++ b/doc/forum/could_not_read_from_remote_repository/comment_1_27d4d1556a80c06505ed3d8a9422d082._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-26T20:18:26Z"
+ content="""
+The problem seems to be on your desktop computer. /home/max/.ssh/git-annex-shell is a script that is created if you install git-annex from the standalone tarball (assuming you're using linux?). It seems that your desktop has that script, but you must have deleted that instalation of git-annex (perhaps you switched to installing it some other way), so the script doesn't work. As long as you have git-annex-shell in your PATH somehow, you can just remove /home/max/.ssh/git-annex-shell
+"""]]
diff --git a/doc/forum/dot_git_slash_annex_slash_tmp/comment_11_b1f717342c1c8ea42a451caa2d936622._comment b/doc/forum/dot_git_slash_annex_slash_tmp/comment_11_b1f717342c1c8ea42a451caa2d936622._comment
new file mode 100644
index 000000000..c882a8573
--- /dev/null
+++ b/doc/forum/dot_git_slash_annex_slash_tmp/comment_11_b1f717342c1c8ea42a451caa2d936622._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="stoile"
+ ip="2a01:198:242:0:219:66ff:fef2:c021"
+ subject="Same problem here"
+ date="2013-11-16T12:10:55Z"
+ content="""
+I got the same problem on linux. Under what circumstances does \"git annex unused\" not find files in .git/annex/tmp? Maybe it is possible to improve \"git annex unused\"...
+"""]]
diff --git a/doc/forum/dot_git_slash_annex_slash_tmp/comment_12_e2c6ad99333018c8c46e736da416b8ef._comment b/doc/forum/dot_git_slash_annex_slash_tmp/comment_12_e2c6ad99333018c8c46e736da416b8ef._comment
new file mode 100644
index 000000000..153a617b5
--- /dev/null
+++ b/doc/forum/dot_git_slash_annex_slash_tmp/comment_12_e2c6ad99333018c8c46e736da416b8ef._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmkXtBdMgE1d9nCz2iBc4f85xh4izZ_auU"
+ nickname="Ulrich"
+ subject="Wow. Found >180 GB of data in annex/tmp"
+ date="2013-11-24T21:53:29Z"
+ content="""
+… no wonder my disk was filling up. On Mac OS X 10.9…
+"""]]
diff --git a/doc/forum/dropping_files_not_working_when_using_git_annex_assistant.txt b/doc/forum/dropping_files_not_working_when_using_git_annex_assistant.txt
new file mode 100644
index 000000000..05680a740
--- /dev/null
+++ b/doc/forum/dropping_files_not_working_when_using_git_annex_assistant.txt
@@ -0,0 +1,18 @@
+Just playing with git-annex which looks great so far, but I noticed that when you make use off "git annex assistant" to watch and sync your repo with the remote it doesn't drop files anymore. They just stay in the repo.
+
+What I have is the following:
+
+- 2 repo's in direct mode
+- they both have each other as remote
+- they're synced and stay synced with the assistant daemon running (in both repo's started "git annex assistant")
+- is see changes coming and precessed, so so far so good.
+
+Then I drop in one repo a path for instance like : git annex drop iso
+Afterwards I still see the files (and contents) in that repo. New files in the iso path are still synced to the other and vise versa.
+
+Then I kill the assistant on both side's and drop the path again. This time it's dropped as expected and the contents of the file in the iso path are gone.
+Starting the assistant again brings is back though :(
+
+I really liked the assistant feature and possibility of dropping the files from one repo, but they don't seem to work together.
+
+Is this a bur or expected behaviour? I think the latter since the assistant also does the git annex get commands so sounds logical?
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers.mdwn b/doc/forum/git-annex_assistant_with_2_dedicated_servers.mdwn
new file mode 100644
index 000000000..1544b14ef
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers.mdwn
@@ -0,0 +1,11 @@
+Hello,
+
+I am looking for a solution to replicate lots of files between 2 servers (with dedicated IP address) over WAN. (I already looked at GlusterFS, DRBD, Bittorent-Sync and ownCloud, but comments are welcome). Now I am evaluating git-annex but it is (kind of) hard to get the concepts as I am not familiar with git.
+
+I could already connect the servers by following the steps of "remote sharing walkthrough" but I feel that using a 3rd special node (as "transfer repository" / rsync or ssh) is an overhead and should not be needed. But no matter how hard I tried, I couldn't make the 2 servers do a sync without a special node. 
+
+Could you please give me a hint how to do it? Or even better, some detailed steps. :)
+
+Thanks,
+
+David
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_10_533ade2215c879cd46782fd66a97b167._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_10_533ade2215c879cd46782fd66a97b167._comment
new file mode 100644
index 000000000..ec7dc0f86
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_10_533ade2215c879cd46782fd66a97b167._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="comment 10"
+ date="2013-11-16T23:15:49Z"
+ content="""
+Great. Understood. :) Thanks.
+
+Although there is one more thing that I don't really understand. Why do we need 2 repositories. In my mind (without knowing git) I thout it would work with one repository, where both server1 and server2 can upload/download files and they got synced through this. 
+
+    server1 <-> repository (somewhere, eother server1 or server2) <-> server2
+
+Now they use different repositories and I don't get why. Also I don't get how conflict-handling can be done if there are 2 repositories for the 2 transfer-ways.
+
+Sorry to bother you with this.
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_11_c9ae51d7b772cf7a91d90925f74d2b60._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_11_c9ae51d7b772cf7a91d90925f74d2b60._comment
new file mode 100644
index 000000000..f614d066d
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_11_c9ae51d7b772cf7a91d90925f74d2b60._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 11"
+ date="2013-11-16T23:25:26Z"
+ content="""
+When using git, each place you access your files is a separate repository. Thus, you have:
+
+server1 (repository) <--> server2 (repository) 
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_12_41fbee0ec9bc890e309bcd48a58c3851._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_12_41fbee0ec9bc890e309bcd48a58c3851._comment
new file mode 100644
index 000000000..d707de6e1
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_12_41fbee0ec9bc890e309bcd48a58c3851._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="comment 12"
+ date="2013-11-18T11:25:06Z"
+ content="""
+Hello,
+
+Thanks for your help and explanation. Now I had some time to test git-annex and I had a sad experience. I tried to sync the files from server1 to server2 (as described before). We are talking about 87000 small files (these are maildir folders and each file is an e-mail) with the total size of 19 Gbytes. After a few hours git-annex assistant consumed all memory on both servers ... and then all swap ... and then kernel killed git-annex. The servers have 512 MB RAM and 1 GB swap.
+
+According to the Scalability page (http://git-annex.branchable.com/scalability/) the \"memory usage should be constant\" and I am sure I didn't run \"git-annex unused\".
+
+Is this memory consumption normal or it might be a bug? What shall we do?
+
+Thanks,
+
+David
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_13_571cffc0beb8ba5fc936db6971cd3d62._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_13_571cffc0beb8ba5fc936db6971cd3d62._comment
new file mode 100644
index 000000000..aefe98813
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_13_571cffc0beb8ba5fc936db6971cd3d62._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="comment 13"
+ date="2013-11-19T09:17:26Z"
+ content="""
+Please tell me if/how I can help you. For example if you need access to servers to test...
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_1_53a79af2d8e3abe50b983bf91972b8f2._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_1_53a79af2d8e3abe50b983bf91972b8f2._comment
new file mode 100644
index 000000000..f6f058988
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_1_53a79af2d8e3abe50b983bf91972b8f2._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-16T17:42:48Z"
+ content="""
+The [[assistant/remote sharing walkthrough]] assumes that the computers are not servers, so they might not be turned on at the same time, and cannot directly contect each other.
+
+With 2 servers, it's much simpler. Just add a git remote on each pointing at the git repository on the other server, and run the git-annex assistant on both to keep them in sync.
+
+You can add the git remote with `git remote add otherserver ssh://otherserver/path/to/repo`, or you can use the webapp to do it (Add another repository -> Remote server)
+
+(If your WAN puts the servers on the same virtual subnet, ie a VPN, you can also probably use local pairing over the WAN to get to the same setup by a different route.)
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_2_c0ba3e8b7fbf8a5ed718001cec8df676._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_2_c0ba3e8b7fbf8a5ed718001cec8df676._comment
new file mode 100644
index 000000000..8c4bb5922
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_2_c0ba3e8b7fbf8a5ed718001cec8df676._comment
@@ -0,0 +1,35 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="still need some clarification"
+ date="2013-11-16T22:02:46Z"
+ content="""
+Hello,
+
+Thanks for your reply. I guessed that there is an easier, direct way to do it. But unfortunately I still need some clarification. This is how I tried:
+
+1. Cleared everything to start from scratch.
+2. I started git-annex on server1: screen git annex webapp --listen=server1_ip, opened the webapp and created the local repository /media/mail
+3. I configured the XMPP account on server1.
+4. Started git-annex on server2: screen git annex webapp --listen=server2_ip, opened the webapp and created the local repository /media/mail
+5. I configured the XMPP account on server2.
+
+And here comes the confusing part:
+
+6. On server1 I clicked Add another repository / Remote server: and configured ssh server2 to the same folder: /media/mail. I chose client repository group instead of transfer. (I am not sure if I did it right) ... but server1 started sync-ing.
+7. On server2 I clicked Add another repository / Remote server: and configured ssh server1 to the same folder: /media/mail. Then I received an error message:
+
+    Failed to make repository
+    Something went wrong setting up the repository on the remote server.
+    
+    Transcript:
+    
+    init  error: could not lock config file /media/mail-test/mail/.git/config: Permission denied
+    git-annex: git [Param \"config\",Param \"annex.version\",Param \"3\"] failed
+
+Cold you please help me where I did wrong?
+
+Thanks,
+
+David
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_3_60c39bc8ef74e80e72381d514b6dd223._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_3_60c39bc8ef74e80e72381d514b6dd223._comment
new file mode 100644
index 000000000..f9e405b70
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_3_60c39bc8ef74e80e72381d514b6dd223._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 3"
+ date="2013-11-16T22:18:20Z"
+ content="""
+It seems to me that you probably told git-annex to log into server2 as a user that does not have write access to sever2:/media/mail. Check the username field in the remote repository form.
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_4_6241120b4325c905661ef72881f4d7af._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_4_6241120b4325c905661ef72881f4d7af._comment
new file mode 100644
index 000000000..bb7c19389
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_4_6241120b4325c905661ef72881f4d7af._comment
@@ -0,0 +1,20 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="still need some clarification"
+ date="2013-11-16T22:31:07Z"
+ content="""
+Hey,
+
+Yes, you were right. The ssh user did not have privileges to read/write the folder. Now I have corrected this issue and things started sync-ing.
+
+But I am afraid, this is not exactly the thing I wanted to achieve. My goal was to sync from folder to folder ... and not from folder to repository both ways.
+
+So, what I would like to do is that if I create a file at server1 (e.g. /media/mail/test01.txt) then it should appear at server2 at /media/mail/test01.txt.
+
+How can I achieve this?
+
+Thanks a lot.
+
+David
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_5_cab00b8fa195340f4d3fdaf5af975b57._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_5_cab00b8fa195340f4d3fdaf5af975b57._comment
new file mode 100644
index 000000000..179a65a99
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_5_cab00b8fa195340f4d3fdaf5af975b57._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 5"
+ date="2013-11-16T22:55:34Z"
+ content="""
+Well, that's what should happen. What behavior are you seeing? What version of git-annex are you using?
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_6_e24df9a1c68724a912b8ac6533d9bd25._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_6_e24df9a1c68724a912b8ac6533d9bd25._comment
new file mode 100644
index 000000000..a28e947dd
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_6_e24df9a1c68724a912b8ac6533d9bd25._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="comment 6"
+ date="2013-11-16T22:58:15Z"
+ content="""
+Hello,
+
+Yes, meanwhile files started appearing. :) Maybe I just did not wait enough time.
+
+So, I have just one more question. Shall I set the remote ssh repositories to client or transfer? I read the docs and understand the difference, but in my case I simply cannot decide. 
+
+Thanks a lot for your hard work and great support. 
+
+David
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_7_ace3dc7c60c710a04b0a587206b341c4._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_7_ace3dc7c60c710a04b0a587206b341c4._comment
new file mode 100644
index 000000000..c41fe492f
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_7_ace3dc7c60c710a04b0a587206b341c4._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 7"
+ date="2013-11-16T23:04:29Z"
+ content="""
+In your situation, you do not have or need a repository whose only job is to transfer files between two other client repositories. So the right choice for your repositories is client -- or something else possibly -- but almost certainly not transfer.
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_8_9a96bc970a17ed62b0ceb7aa3f0a6f8b._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_8_9a96bc970a17ed62b0ceb7aa3f0a6f8b._comment
new file mode 100644
index 000000000..1d0f1db52
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_8_9a96bc970a17ed62b0ceb7aa3f0a6f8b._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="David"
+ ip="178.21.48.117"
+ subject="comment 8"
+ date="2013-11-16T23:09:32Z"
+ content="""
+Okay. One last question. Could you please help me understand how this sync works now? 
+
+So for example if I save a file on server1, it gets pushed to server2's repository. But how is it translated back to a normal file from the repository?
+
+And in this case will this file be on server2's repository as well (so are there 2 copies on server2, one in the repository and one human-readabl)?
+
+Thanks!
+"""]]
diff --git a/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_9_ea88e0696f6e25e6904248a323f6cc36._comment b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_9_ea88e0696f6e25e6904248a323f6cc36._comment
new file mode 100644
index 000000000..cafac1077
--- /dev/null
+++ b/doc/forum/git-annex_assistant_with_2_dedicated_servers/comment_9_ea88e0696f6e25e6904248a323f6cc36._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 9"
+ date="2013-11-16T23:11:58Z"
+ content="""
+Since you created these repositories with the webapp, they default to using [[direct_mode]]. git-annex handles putting the files in place when they are transferred to the repository. Only 1 copy is made, there is no separate copy in the repository.
+"""]]
diff --git a/doc/forum/git_annex_test_on_windows.mdwn b/doc/forum/git_annex_test_on_windows.mdwn
new file mode 100644
index 000000000..4e2f8dea6
--- /dev/null
+++ b/doc/forum/git_annex_test_on_windows.mdwn
@@ -0,0 +1,5 @@
+is it worth sharing back git annex test failures occourring on some windows setup ?
+i'm having 3 failures, what kind of report can i produce shall it be of any use ?
+is it enough a test log coming from git annex test > test.log 2>&1 ?
+thanks again
+
diff --git a/doc/forum/git_annex_test_on_windows/comment_1_258ac5cfa2f5d24e737d94dc48f06899._comment b/doc/forum/git_annex_test_on_windows/comment_1_258ac5cfa2f5d24e737d94dc48f06899._comment
new file mode 100644
index 000000000..d7968c16e
--- /dev/null
+++ b/doc/forum/git_annex_test_on_windows/comment_1_258ac5cfa2f5d24e737d94dc48f06899._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-15T20:53:17Z"
+ content="""
+Yes, it's fine to file a bug about test failures. Be sure you try with a current autobuild.
+
+The redirection you show would work on linux, I don't know about windows. But capturing a transcript of the test output is certainly what I need.
+"""]]
diff --git a/doc/forum/lost_in_walkthrough....txt b/doc/forum/lost_in_walkthrough....txt
new file mode 100644
index 000000000..89f4af026
--- /dev/null
+++ b/doc/forum/lost_in_walkthrough....txt
@@ -0,0 +1,78 @@
+I'm trying to follow the steps of the "walkthrough" but I'm experiencing the following issue: when
+I sync one repository and do "git annex get ." I don't get the files from the other repository.
+Here is the transcript of the steps I followed - I've put them in a script (ga.sh) so I can replay
+them and show them on the shell while executing.
+Basically I have two repositories, "/tmp/a/annex" and "/tmp/b/annex", the second cloned from
+the first. All the other steps are the same as in the walkthrough.
+-----------------------------------
+> bash -x ga.sh 
++ cd /tmp
++ mkdir a
++ mkdir b
++ cd a
++ mkdir annex
++ cd annex
++ git init
+Initialized empty Git repository in /tmp/a/annex/.git/
++ git annex init a
+init a ok
+(Recording state in git...)
++ cd /tmp/b
++ git clone /tmp/a/annex
+Cloning into 'annex'...
+done.
+warning: remote HEAD refers to nonexistent ref, unable to checkout.
+
++ cd annex
++ git annex init b
+init b ok
+(Recording state in git...)
++ git remote add a /tmp/a/annex
++ cd /tmp/a/annex
++ git remote add b /tmp/b/annex
++ dd if=/dev/urandom of=first bs=1024 count=1
+1+0 records in
+1+0 records out
+1024 bytes (1.0 kB) copied, 9.9167e-05 s, 10.3 MB/s
++ dd if=/dev/urandom of=second bs=1024 count=1
+1+0 records in
+1+0 records out
+1024 bytes (1.0 kB) copied, 0.000241635 s, 4.2 MB/s
++ git annex add .
+add first (checksum...) ok
+add second (checksum...) ok
+(Recording state in git...)
++ git commit -am added
+[master (root-commit) 5078564] added
+ 2 files changed, 2 insertions(+)
+ create mode 120000 first
+ create mode 120000 second
++ git mv first e
++ mkdir x
++ git mv second x
++ git commit -m moved
+fix x/second ok
+(Recording state in git...)
+[master 422492d] moved
+ 3 files changed, 1 insertion(+), 1 deletion(-)
+ rename first => e (100%)
+ delete mode 120000 second
+ create mode 120000 x/second
++ cd /tmp/b/annex
++ git annex sync a
+(merging origin/git-annex into git-annex...)
+(Recording state in git...)
+commit  
+ok
+git-annex: no branch is checked out
++ git annex get .
+-------------------
+
+The last "git annex get ." does not retrieve the files in /tmp/a/annex ... why?
+I guess the issue starts when cloning /tmp/a/annex where no commit was done.
+
+Emanuele
+
+PS: I'm using git v1.7.9.5 (ubuntu 12.04) and the latest git-annex static binary
+downloaded a few minutes ago from the git-annex website.
+
diff --git a/doc/forum/lost_in_walkthrough.../comment_1_51b703b961ca762f0359e1c169f1ee75._comment b/doc/forum/lost_in_walkthrough.../comment_1_51b703b961ca762f0359e1c169f1ee75._comment
new file mode 100644
index 000000000..a5c574b4a
--- /dev/null
+++ b/doc/forum/lost_in_walkthrough.../comment_1_51b703b961ca762f0359e1c169f1ee75._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-02T19:32:50Z"
+ content="""
+I have fixed `git annex sync` to work even when run in a repository with no master branch. 
+"""]]
diff --git a/doc/forum/lost_in_walkthrough.../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment b/doc/forum/lost_in_walkthrough.../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment
new file mode 100644
index 000000000..4a8110eb4
--- /dev/null
+++ b/doc/forum/lost_in_walkthrough.../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawn2MI-Ci-bS9W5NITngsBJiL8LqWYcJ458"
+ nickname="Emanuele"
+ subject="comment 2"
+ date="2013-11-02T23:36:54Z"
+ content="""
+Great thanks! I'm glad my feedback helped improve git-annex!
+
+<https://github.com/joeyh/git-annex/commit/bc18cde32589cf53080c399e81b5680e4b>af6cef
+
+"""]]
diff --git a/doc/forum/not_getting_file_contents/comment_1_4a0f7f4de9c9bc4d13db033cb75d20af._comment b/doc/forum/not_getting_file_contents/comment_1_4a0f7f4de9c9bc4d13db033cb75d20af._comment
index b9c9d7e45..e03ec333a 100644
--- a/doc/forum/not_getting_file_contents/comment_1_4a0f7f4de9c9bc4d13db033cb75d20af._comment
+++ b/doc/forum/not_getting_file_contents/comment_1_4a0f7f4de9c9bc4d13db033cb75d20af._comment
@@ -4,7 +4,7 @@
  subject="comment 1"
  date="2013-07-11T16:06:59Z"
  content="""
-That certianly shouldn't be happening! 
+That certainly shouldn't be happening! 
 
 Are these computers syncing via local pairing, or are you using a transfer remote, and if so, which one?
 """]]
diff --git a/doc/forum/performance_and_multiple_replication_problems/comment_1_a2cdf1a4840f099f6bc941fd8de966c7._comment b/doc/forum/performance_and_multiple_replication_problems/comment_1_a2cdf1a4840f099f6bc941fd8de966c7._comment
index 7791950f6..aab0ec17f 100644
--- a/doc/forum/performance_and_multiple_replication_problems/comment_1_a2cdf1a4840f099f6bc941fd8de966c7._comment
+++ b/doc/forum/performance_and_multiple_replication_problems/comment_1_a2cdf1a4840f099f6bc941fd8de966c7._comment
@@ -12,5 +12,5 @@ It would be possible to disable that scan, but at the expense of not being able
 
 I don't quite understand what you mean with problem #2. If files were repeatedly being uploaded or downloaded, that have already been sent, that would be a bug. Please file a bug report with full debug logs if that is the case.
 
-Which topology is best? I think the best way is to start with the one you like, and if it doesn't work well, add more links between repositories. A star topology will certianly work ok. A mesh can work ok but can be hard to maintain.
+Which topology is best? I think the best way is to start with the one you like, and if it doesn't work well, add more links between repositories. A star topology will certainly work ok. A mesh can work ok but can be hard to maintain.
 """]]
diff --git a/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_5_7abbbe7db3988a2d239d11b0a4c597e7._comment b/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_5_7abbbe7db3988a2d239d11b0a4c597e7._comment
new file mode 100644
index 000000000..651fc8144
--- /dev/null
+++ b/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_5_7abbbe7db3988a2d239d11b0a4c597e7._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="stoile"
+ ip="2a01:198:242:0:219:66ff:fef2:c021"
+ subject="Error with .git/annex as a symlink"
+ date="2013-11-16T12:20:58Z"
+ content="""
+I had my git annex directory on a ssd and .git/annex on a hdd (using a symlink). I got errors when adding files because a move failed. I forgot to copy the error message. When I had .git/annex/objects on a hdd, everything worked as expected, there were no problems.
+
+So what exactly will go wrong if I only have this one subdirectory on another filesystem?
+"""]]
diff --git a/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_6_46bd45fdc25d9c583f4ebe3a9730ab9f._comment b/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_6_46bd45fdc25d9c583f4ebe3a9730ab9f._comment
new file mode 100644
index 000000000..0c0e3e495
--- /dev/null
+++ b/doc/forum/performance_improvement:_git_on_ssd__44___annex_on_spindle_disk/comment_6_46bd45fdc25d9c583f4ebe3a9730ab9f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="stoile"
+ ip="2a01:198:242:0:219:66ff:fef2:c021"
+ subject="Bug report answering my question"
+ date="2013-11-17T10:28:40Z"
+ content="""
+My question was answered in <http://git-annex.branchable.com/bugs/not_possible_to_have_annex_on_a_separate_filesystem/>.
+"""]]
diff --git a/doc/forum/preferred_content.mdwn b/doc/forum/preferred_content.mdwn
new file mode 100644
index 000000000..b4c215328
--- /dev/null
+++ b/doc/forum/preferred_content.mdwn
@@ -0,0 +1,11 @@
+Hello all,
+
+I'm trying to use "preferred content" with git-annex but I suspect that my version doesn't provide it.
+
+I'm using Debian "wheezy" that packs git-annex 3.20120629.
+
+I appreciate any help you can give.
+
+Thanks.
+
+Zaka.
diff --git a/doc/forum/preferred_content/comment_1_9c9e5f2ee5ae4d8459358ad16f879ef1._comment b/doc/forum/preferred_content/comment_1_9c9e5f2ee5ae4d8459358ad16f879ef1._comment
new file mode 100644
index 000000000..24de5840b
--- /dev/null
+++ b/doc/forum/preferred_content/comment_1_9c9e5f2ee5ae4d8459358ad16f879ef1._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-07T18:38:22Z"
+ content="""
+The first version of git-annex to support preferred content settings was 3.20121009.
+
+There is a quite up-to-date backport available for Debian stable.
+"""]]
diff --git a/doc/forum/pure_git-annex_only_workflow/comment_8_6e5b42fdb7801daadc0b3046cbc3d51e._comment b/doc/forum/pure_git-annex_only_workflow/comment_8_6e5b42fdb7801daadc0b3046cbc3d51e._comment
index d33a296ca..67953860a 100644
--- a/doc/forum/pure_git-annex_only_workflow/comment_8_6e5b42fdb7801daadc0b3046cbc3d51e._comment
+++ b/doc/forum/pure_git-annex_only_workflow/comment_8_6e5b42fdb7801daadc0b3046cbc3d51e._comment
@@ -4,7 +4,7 @@
  subject="comment 8"
  date="2011-12-19T18:29:01Z"
  content="""
-I don't mind changing the behavior of git-annex sync, certianly..
+I don't mind changing the behavior of git-annex sync, certainly..
 
 Looking thru git's documentation, I found some existing configuration that could be reused following your idea.
 There is a remote.name.skipDefaultUpdate and a remote.name.skipFetchAll. Though both have to do with fetches, not pushes.
diff --git a/doc/forum/reinstalled_os__44___cloned_annex__44___does_not_recognize_remote/comment_2_1f0f4a1dc89643cee81ff7199b55e747._comment b/doc/forum/reinstalled_os__44___cloned_annex__44___does_not_recognize_remote/comment_2_1f0f4a1dc89643cee81ff7199b55e747._comment
new file mode 100644
index 000000000..f38c0c752
--- /dev/null
+++ b/doc/forum/reinstalled_os__44___cloned_annex__44___does_not_recognize_remote/comment_2_1f0f4a1dc89643cee81ff7199b55e747._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmBhQgaA5QrFwT67-Bo0qPIx0HD9roDrso"
+ nickname="Paul"
+ subject="comment 2"
+ date="2013-11-20T11:20:13Z"
+ content="""
+The problem was just a missing git remote. Sorry & thanks
+"""]]
diff --git a/doc/forum/rsyncing_.git__47__annex__47__objects.mdwn b/doc/forum/rsyncing_.git__47__annex__47__objects.mdwn
new file mode 100644
index 000000000..876b5e04a
--- /dev/null
+++ b/doc/forum/rsyncing_.git__47__annex__47__objects.mdwn
@@ -0,0 +1,24 @@
+In short: is it safe to rsync .git/annex/objects/ to other clones?
+
+I'm in the process of migrating a lot of my files to a new backend.  Most them
+still use the old non-file-size-tracking SHA1 backend from when WORM was the
+default.  I have multiple clones that each use about 460 GB of their 500 GB
+drives.
+
+I've noticed that git-annex creates hardlinks to migrated content in
+.git/annex/objects, so I'm able to migrate all content despite only having 40
+GB of free space.  Excellent.
+
+Now I'm planning to `rsync -a --hard-links .git/annex/objects/
+${CLONE}/.git/annex/objects/` to recreate the hardlinks and save space on the
+clones as well.  If I `fsck` afterwards, this should be fine, right?
+
+I've tried this with a test repository and it works but I'd like to be extra
+sure that I'm not missing something crucial.
+
+The alternatives that I'm aware of are:
+
+ * making space first: `git annex dropunused "1-20000"` and `git annex get .`
+ * running `git annex migrate` in each clone.
+
+I expect rsync to be safer and faster than these alternatives.
diff --git a/doc/forum/rsyncing_.git__47__annex__47__objects/comment_1_25eb9f7be5730337b9efd96dce9efd2e._comment b/doc/forum/rsyncing_.git__47__annex__47__objects/comment_1_25eb9f7be5730337b9efd96dce9efd2e._comment
new file mode 100644
index 000000000..8d9e22a7e
--- /dev/null
+++ b/doc/forum/rsyncing_.git__47__annex__47__objects/comment_1_25eb9f7be5730337b9efd96dce9efd2e._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-16T17:36:48Z"
+ content="""
+As long as you fsck afterwards, this is fine.
+
+You might want to `git annex fsck --all` in case you have objects for old versions of files.
+"""]]
diff --git a/doc/forum/rsyncing_.git__47__annex__47__objects/comment_2_d7ceae666c8a1951021d3c6e6ac39a11._comment b/doc/forum/rsyncing_.git__47__annex__47__objects/comment_2_d7ceae666c8a1951021d3c6e6ac39a11._comment
new file mode 100644
index 000000000..f9c449f5e
--- /dev/null
+++ b/doc/forum/rsyncing_.git__47__annex__47__objects/comment_2_d7ceae666c8a1951021d3c6e6ac39a11._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="gernot"
+ ip="89.0.237.214"
+ subject="comment 2"
+ date="2013-11-18T15:09:59Z"
+ content="""
+Thanks for the confirmation, Joey!  I also wouldn't have thought of `--all`.
+"""]]
diff --git a/doc/forum/s3_vs_ssh_Performance_Problems.mdwn b/doc/forum/s3_vs_ssh_Performance_Problems.mdwn
new file mode 100644
index 000000000..5176e196f
--- /dev/null
+++ b/doc/forum/s3_vs_ssh_Performance_Problems.mdwn
@@ -0,0 +1,8 @@
+I backup/sync my music using annex. I used to have one repo with 3 clones, one full copy on my vps, one full copy and one partial copy on my laptops. I decided to move all data to s3. Declared my vps repo dead, purged history (I do not care about history for this particular repo) pushed the git repo to a different computer (bare repo no data) and data to s3 (gpg encrypted). I've just finished uploading all files (around 200gb) couple files failed during the initial upload so I did a `git annex copy --quiet --to mys3 --fast` this command used to take 15 20 secs on my laptop when sending data to vps using ssh but now it took 2 hours to complete (pushing mem usage to 90%).
+
+I have one other repo (1.5gb in size 42k files using indirect mode, data gpg encrypted on s3) using the same setup except this repos content has always been on s3  i had the same behavior on this repo too. adding a file and running a copy to push content to s3 took couple hours even if I add a single 1kb file. I used to blame my hard drive, damn thing is slow but now I think this is related to s3. is there any workaround for this?
+
+Both machines are using,
+
+    git-annex version: 4.20130913-gd20a4f2
+    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP Feeds Quvi
diff --git a/doc/forum/s3_vs_ssh_Performance_Problems/comment_1_65f064f09d7850abecab97007b0d30f0._comment b/doc/forum/s3_vs_ssh_Performance_Problems/comment_1_65f064f09d7850abecab97007b0d30f0._comment
new file mode 100644
index 000000000..aa3e06cc0
--- /dev/null
+++ b/doc/forum/s3_vs_ssh_Performance_Problems/comment_1_65f064f09d7850abecab97007b0d30f0._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmBUR4O9mofxVbpb8JV9mEbVfIYv670uJo"
+ nickname="Justin"
+ subject="comment 1"
+ date="2013-11-21T04:09:15Z"
+ content="""
+Is
+
+    git annex copy --not --in mys3 --to mys3 .
+
+any faster?
+"""]]
diff --git a/doc/forum/s3_vs_ssh_Performance_Problems/comment_2_baaf2384d9196077268e9ca9bbe3b871._comment b/doc/forum/s3_vs_ssh_Performance_Problems/comment_2_baaf2384d9196077268e9ca9bbe3b871._comment
new file mode 100644
index 000000000..f54e49b2b
--- /dev/null
+++ b/doc/forum/s3_vs_ssh_Performance_Problems/comment_2_baaf2384d9196077268e9ca9bbe3b871._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://me.yahoo.com/a/FHnTlSBo1eCGJRwueeKeB6.RCaPbGMPr5jxx8A--#ce0d8"
+ nickname="Hamza"
+ subject="comment 2"
+ date="2013-11-21T17:47:57Z"
+ content="""
+No difference. Both take roughly the same time but I did time a couple of runs with both commands they usually take 3 to 5 minutes to complete. Maybe git did something behind the scenes like gc? But still slower than it used to be. My other repo (one with 42k files) still takes a 2 hours.
+"""]]
diff --git a/doc/forum/s3_vs_ssh_Performance_Problems/comment_3_dc44be42070c073d150c476406e9b425._comment b/doc/forum/s3_vs_ssh_Performance_Problems/comment_3_dc44be42070c073d150c476406e9b425._comment
new file mode 100644
index 000000000..cbd460818
--- /dev/null
+++ b/doc/forum/s3_vs_ssh_Performance_Problems/comment_3_dc44be42070c073d150c476406e9b425._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmBUR4O9mofxVbpb8JV9mEbVfIYv670uJo"
+ nickname="Justin"
+ subject="comment 3"
+ date="2013-11-22T20:21:11Z"
+ content="""
+Well it's not related to s3... that copy command won't even do any network traffic if there is nothing to copy.  I have a similarly configured annex with 4500 files and that command takes 10 seconds to run.
+
+I do remember there being a recent fix that reduced the algorithmic complexity of an operation, but I forget which.
+"""]]
diff --git a/doc/forum/speed_up_assistant_startup_on_large_repositories.mdwn b/doc/forum/speed_up_assistant_startup_on_large_repositories.mdwn
new file mode 100644
index 000000000..e43476c7b
--- /dev/null
+++ b/doc/forum/speed_up_assistant_startup_on_large_repositories.mdwn
@@ -0,0 +1 @@
+Starting the assistant on a repository with a huge amount of files (f.e. `annexed files in working tree: 22087`) takes a very long time. Is there a way to speed it up? F.e. just checking the file stamps and comparing them with the last assistant run time? Checking if the files are modified could be done with the regular repository check. Thoughts?
diff --git a/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_1_5ba637a0f6d01ba24fe25e6265134e0a._comment b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_1_5ba637a0f6d01ba24fe25e6265134e0a._comment
new file mode 100644
index 000000000..0abe4dec8
--- /dev/null
+++ b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_1_5ba637a0f6d01ba24fe25e6265134e0a._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-05T16:43:26Z"
+ content="""
+Checking the time stamps is what it does.
+
+How long is a very long time?
+"""]]
diff --git a/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_2_d65746697977f8971a4b59f5b413f926._comment b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_2_d65746697977f8971a4b59f5b413f926._comment
new file mode 100644
index 000000000..e6915d232
--- /dev/null
+++ b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_2_d65746697977f8971a4b59f5b413f926._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawne_amN4fko4p5cRY_9EYwaYuJKNn7LRio"
+ nickname="Tobias"
+ subject="measuring how-to"
+ date="2013-11-08T16:55:58Z"
+ content="""
+How can I measure how much time the startup scan takes? I tried to find it out using the debug log, but couldn't find any usable notice when the startup scan was finished. Maybe this two lines?
+
+    [...]
+    [2013-11-08 16:00:45 CET] Watcher: Performing startup scan
+    [...]
+    [2013-11-08 16:15:30 CET] Watcher: watching 
+"""]]
diff --git a/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_3_be6c4fe5a0c745688438b716973791cc._comment b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_3_be6c4fe5a0c745688438b716973791cc._comment
new file mode 100644
index 000000000..d3fe6ef4c
--- /dev/null
+++ b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_3_be6c4fe5a0c745688438b716973791cc._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="108.236.230.124"
+ subject="comment 3"
+ date="2013-11-08T17:04:23Z"
+ content="""
+That's right.
+
+15 minutes is certainly a very long time.
+
+Is this on a slow spinning disk? USB disk?
+"""]]
diff --git a/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_4_a07472338a08c068a9b88b2176fc2bee._comment b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_4_a07472338a08c068a9b88b2176fc2bee._comment
new file mode 100644
index 000000000..41e69ab1e
--- /dev/null
+++ b/doc/forum/speed_up_assistant_startup_on_large_repositories/comment_4_a07472338a08c068a9b88b2176fc2bee._comment
@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawniayrgSdVLUc3c6bf93VbO-_HT4hzxmyo"
+ nickname="Tobias"
+ subject="comment 4"
+ date="2013-11-17T17:28:06Z"
+ content="""
+The mentioned repository is stored on spinning disk.
+Maybe it would help to store the .git directory on an SSD, but I'm not sure how to do it.
+"""]]
diff --git a/doc/forum/unsynced_folder.mdwn b/doc/forum/unsynced_folder.mdwn
new file mode 100644
index 000000000..ceb04011e
--- /dev/null
+++ b/doc/forum/unsynced_folder.mdwn
@@ -0,0 +1,3 @@
+If I have an archive with a lot of big files, is it possible to get one of them without using the command line, and without it popping up on other clients of that repository?
+Is it possible to have a folder that will not be synced with other clients but will still download the file when i copy it from archive?
+.gitignore probably wont work because that will not get the file from archive.
diff --git a/doc/forum/webapp_listen_port_with_autostart/comment_2_39664f833dedc1a4fe083eec9bc4a7cd._comment b/doc/forum/webapp_listen_port_with_autostart/comment_2_39664f833dedc1a4fe083eec9bc4a7cd._comment
new file mode 100644
index 000000000..0d48ba825
--- /dev/null
+++ b/doc/forum/webapp_listen_port_with_autostart/comment_2_39664f833dedc1a4fe083eec9bc4a7cd._comment
@@ -0,0 +1,75 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmiqeXJtP04fzHOjXs17kHO33v7dWR2xwA"
+ nickname="Jaco"
+ subject="Init Script"
+ date="2013-11-23T08:28:32Z"
+ content="""
+Hi Joey,
+
+Could you help out with writing an init.d script to safely start and stop the webapp on a headless server? 
+I made an attempt below based on examples from the internet, but have no idea if it will work.
+
+	#!/bin/bash
+	# git-annex
+	# chkconfig: 345 20 80
+	# description: Git Annex WebApp startup and shutdown script.
+	# processname: git-annex
+	
+	
+	DAEMON=git-annex webapp
+	
+	NAME=git-annex
+	DESC=\"Git Annex WebApp init script\"
+	PIDFILE=/var/run/$NAME.pid
+	SCRIPTNAME=/etc/init.d/$NAME
+	
+	case \"$1\" in
+	start)
+		printf \"%-50s\" \"Starting $NAME...\"
+		for dir in $(cat $HOME/.config/git-annex/autostart); do
+			cd $dir
+			PID=`$DAEMON > /dev/null 2>&1 & echo $!`
+			#echo \"Saving PID\" $PID \" to \" $PIDFILE
+		        if [ -z $PID ]; then
+	        		printf \"%s\n\" \"Fail\"
+		        else
+	        		echo $PID > $PIDFILE
+				printf \"%s\n\" \"Ok\"
+			fi
+		done
+	;;
+	status)
+	        printf \"%-50s\" \"Checking $NAME...\"
+	        if [ -f $PIDFILE ]; then
+			for PID in $(cat $PIDFILE); do
+				if [ -z \"`ps axf | grep ${PID} | grep -v grep`\" ]; then
+					printf \"%s\n\" \"Process dead but pidfile exists\"
+				else
+					echo \"Running\"
+				fi
+			done
+	        else
+	            printf \"%s\n\" \"Service not running\"
+	        fi
+	;;
+	stop)
+	        printf \"%-50s\" \"Stopping $NAME\"
+		if [ -f $PIDFILE ]; then
+			for PID in $(cat $PIDFILE); do
+				kill -HUP $PID
+				printf \"%s\n\" \"Ok\"
+			done
+			rm -f $PIDFILE
+	        else
+	            printf \"%s\n\" \"pidfile not found\"
+	        fi
+	;;
+	restart)
+	  	$0 stop
+	  	$0 start
+	;;
+	*)
+	        echo \"Usage: $0 {status|start|stop|restart}\"
+	        exit 1
+	esac
+"""]]
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index d88957f9c..25e1045db 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -103,6 +103,13 @@ subdirectories).
 
   To avoid contacting the remote to check if it has every file, specify `--fast`
 
+* `status` [path ...]`
+
+  Similar to `git status --short`, displays the status of the files in the
+  working tree. Shows files that are not checked into git, files that
+  have been deleted, and files that have been modified. 
+  Particulary useful in direct mode.
+
 * `unlock [path ...]`
 
   Normally, the content of annexed files is protected from being changed.
@@ -253,6 +260,14 @@ subdirectories).
   background, you no longer need to manually run git commands when
   manipulating your files.
 
+  By default, all files in the directory will be added to the repository.
+  (Including dotfiles.) To block some files from being added, use
+  `.gitignore` files.
+  
+  By default, all files that are added are added to the annex, the same
+  as when you run `git annex add`. If you configure annex.largefiles,
+  files that it does not match will instead be added with `git add`.
+
   To not daemonize, run with `--foreground` ; to stop a running daemon,
   run with `--stop`
 
@@ -494,6 +509,7 @@ subdirectories).
   `git annex unused`
 
   You can also specify ranges of numbers, such as "1-1000".
+  Or, specify "all" to drop all unused data.
 
   To drop the data from a remote, specify `--from.`
 
@@ -528,7 +544,7 @@ subdirectories).
   to their local `git-annex` branches. So the forgetfulness will automatically
   propigate out from its starting point until all repositories running
   git-annex have forgotten their old history. (You may need to force
-  git to push the branch to any git repositories not running git-annex.
+  git to push the branch to any git repositories not running git-annex.)
 
 * `repair`
 
@@ -563,10 +579,6 @@ subdirectories).
 
 # QUERY COMMANDS
 
-* `version`
-
-  Shows the version of git-annex, as well as repository version information.
-
 * `find [path ...]`
 
   Outputs a list of annexed files in the specified path. With no path,
@@ -607,23 +619,26 @@ subdirectories).
   To generate output suitable for the gource visualisation program,
   specify `--gource`.
 
-* `status [directory ...]`
+* `info [directory ...]`
 
   Displays some statistics and other information, including how much data
   is in the annex and a list of all known repositories.
 
   To only show the data that can be gathered quickly, use `--fast`.
 
-  When a directory is specified, shows a differently formatted status
+  When a directory is specified, shows a differently formatted info
   display for that directory. In this mode, all of the file matching
   options can be used to filter the files that will be included in
-  the status.
+  the information.
 
   For example, suppose you want to run "git annex get .", but
   would first like to see how much disk space that will use.
   Then run:
 
-        	git annex status --fast . --not --in here
+        	git annex info --fast . --not --in here
+* `version`
+
+  Shows the version of git-annex, as well as repository version information.
 
 * `map`
 
@@ -676,8 +691,8 @@ subdirectories).
   Use this to undo an accidental `git annex add` command. It puts the
   file back how it was before the add.
 
-  Note that for safety, the content of the file remains in the annex (as a
-  hard link), until you use `git annex unused` and `git annex dropunused`.
+  Note that for safety, the content of the file remains in the annex,
+  until you use `git annex unused` and `git annex dropunused`.
 
   This is not the command you should use if you intentionally annexed a
   file and don't want its contents any more. In that case you should use
@@ -698,12 +713,21 @@ subdirectories).
 
 * `pre-commit [path ...]`
 
+  This is meant to be called from git's pre-commit hook. `git annex init`
+  automatically creates a pre-commit hook using this.
+
   Fixes up symlinks that are staged as part of a commit, to ensure they
   point to annexed content. Also handles injecting changes to unlocked
   files into the annex.
 
-  This is meant to be called from git's pre-commit hook. `git annex init`
-  automatically creates a pre-commit hook using this.
+* `update-hook refname olvrev newrev`
+
+  This is meant to be called from git's update hook. `git annex init`
+  automatically creates an update hook using this.
+
+  This denies updates being pushed for the currently checked out branch.
+  While receive.denyCurrentBranch normally prevents that, it does
+  not for fake bare repositories, as used by direct mode.
 
 * `fromkey key file`
 
@@ -788,7 +812,7 @@ subdirectories).
   Rather than the normal output, generate JSON. This is intended to be
   parsed by programs that use git-annex. Each line of output is a JSON
   object. Note that json output is only usable with some git-annex commands,
-  like status and find.
+  like info and find.
 
 * `--debug`
 
@@ -1088,7 +1112,7 @@ Here are all the supported configuration settings.
   up to 500000 keys. If your repository is larger than that,
   you can adjust this to avoid `git annex unused` not noticing some unused
   data files. Increasing this will make `git-annex unused` consume more memory;
-  run `git annex status` for memory usage numbers.
+  run `git annex info` for memory usage numbers.
 
 * `annex.bloomaccuracy`
 
@@ -1096,7 +1120,7 @@ Here are all the supported configuration settings.
   `git annex unused`. The default accuracy is 1000 -- 
   1 unused file out of 1000 will be missed by `git annex unused`. Increasing
   the accuracy will make `git annex unused` consume more memory;
-  run `git annex status` for memory usage numbers.
+  run `git annex info` for memory usage numbers.
 
 * `annex.sshcaching`
 
@@ -1123,6 +1147,21 @@ Here are all the supported configuration settings.
   When set to false, prevents the webapp from reminding you when using
   repositories that lack consistency checks.
 
+* `annex.autoupgrade`
+
+  When set to ask (the default), the webapp will check for new versions
+  and prompt if they should be upgraded to. When set to true, automatically
+  upgrades without prompting (on some supported platforms). When set to
+  false, disables any upgrade checking.
+
+  Note that upgrade checking is only done when git-annex is installed
+  from one of the prebuilt images from its website. This does not
+  bypass eg, a Linux distribution's own upgrade handling code.
+
+  This setting also controls whether to restart the git-annex assistant
+  when the git-annex binary is detected to have changed. That is useful
+  no matter how you installed git-annex.
+
 * `annex.autocommit`
 
   Set to false to prevent the git-annex assistant from automatically
diff --git a/doc/git-recover-repository.mdwn b/doc/git-recover-repository.mdwn
deleted file mode 100644
index dac4a310b..000000000
--- a/doc/git-recover-repository.mdwn
+++ /dev/null
@@ -1,40 +0,0 @@
-# NAME
-
-git-recover-repository - Fix a broken git repository
-
-# SYNOPSIS
-
-git-recover-repository [--force]
-
-# DESCRIPTION
-
-This can fix a corrupt or broken git repository, which git fsck would
-only complain has problems.
-
-It does by deleting all corrupt objects, and retreiving all missing
-objects that it can from the remotes of the repository.
-
-If that is not sufficient to fully recover the repository, it can also
-reset branches back to commits before the corruption happened, delete
-branches that are no longer available due to the lost data, and remove any
-missing files from the index. It will only do this if run with the
-`--force` option, since that rewrites history and throws out missing data.
-Note that the `--force` option never touches tags, even if they are no
-longer usable due to missing data.
-
-After running this command, you will probably want to run `git fsck` to
-verify it fixed the repository. Note that fsck may still complain about
-objects referenced by the reflog, or the stash, if they were unable to be
-recovered. This command does not try to clean up either the reflog or the
-stash.
-
-Since this command unpacks all packs in the repository, you may want to
-run `git gc` afterwards.
-
-# AUTHOR
-
-Joey Hess <joey@kitenet.net>
-
-<http://git-annex.branchable.com/>
-
-Warning: Automatically converted into a man page by mdwn2man. Edit with care
diff --git a/doc/ikiwiki/pagespec.mdwn b/doc/ikiwiki/pagespec.mdwn
new file mode 100644
index 000000000..0f298ad78
--- /dev/null
+++ b/doc/ikiwiki/pagespec.mdwn
@@ -0,0 +1,86 @@
+[[!meta robots="noindex, follow"]]
+To select a set of pages, such as pages that are locked, pages
+whose commit emails you want subscribe to, or pages to combine into a
+blog, the wiki uses a PageSpec. This is an expression that matches
+a set of pages.
+
+The simplest PageSpec is a simple list of pages. For example, this matches
+any of the three listed pages:
+
+	foo or bar or baz
+
+More often you will want to match any pages that have a particular thing in
+their name. You can do this using a glob pattern. "`*`" stands for any part
+of a page name, and "`?`" for any single letter of a page name. So this
+matches all pages about music, and any [[SubPage]]s of the SandBox, but does
+not match the SandBox itself:
+
+	*music* or SandBox/*
+
+You can also prefix an item with "`!`" to skip pages that match it. So to
+match all pages except for Discussion pages and the SandBox:
+
+	* and !SandBox and !*/Discussion
+
+Some more elaborate limits can be added to what matches using these functions:
+
+* "`glob(someglob)`" - matches pages and other files that match the given glob.
+  Just writing the glob by itself is actually a shorthand for this function.
+* "`page(glob)`" - like `glob()`, but only matches pages, not other files
+* "`link(page)`" - matches only pages that link to a given page (or glob)
+* "`tagged(tag)`" - matches pages that are tagged or link to the given tag (or
+  tags matched by a glob)
+* "`backlink(page)`" - matches only pages that a given page links to
+* "`creation_month(month)`" - matches only files created on the given month
+  number
+* "`creation_day(mday)`" - or day of the month
+* "`creation_year(year)`" - or year
+* "`created_after(page)`" - matches only files created after the given page
+  was created
+* "`created_before(page)`" - matches only files created before the given page
+  was created
+* "`internal(glob)`" - like `glob()`, but matches even internal-use 
+  pages that globs do not usually match.
+* "`title(glob)`", "`author(glob)`", "`authorurl(glob)`",
+  "`license(glob)`", "`copyright(glob)`", "`guid(glob)`" 
+  - match pages that have the given metadata, matching the specified glob.
+* "`user(username)`" - tests whether a modification is being made by a
+  user with the specified username. If openid is enabled, an openid can also
+  be put here. Glob patterns can be used in the username. For example, 
+  to match all openid users, use `user(*://*)`
+* "`admin()`" - tests whether a modification is being made by one of the
+  wiki admins.
+* "`ip(address)`" - tests whether a modification is being made from the
+  specified IP address. Glob patterns can be used in the address. For
+  example, `ip(127.0.0.*)`
+* "`comment(glob)`" - matches comments to a page matching the glob.
+* "`comment_pending(glob)`" - matches unmoderated, pending comments.
+* "`postcomment(glob)`" - matches only when comments are being 
+  posted to a page matching the specified glob
+
+For example, to match all pages in a blog that link to the page about music
+and were written in 2005:
+
+	blog/* and link(music) and creation_year(2005)
+
+Note the use of "and" in the above example, that means that only pages that
+match each of the three expressions match the whole. Use "and" when you
+want to combine expression like that; "or" when it's enough for a page to
+match one expression. Note that it doesn't make sense to say "index and
+SandBox", since no page can match both expressions.
+
+More complex expressions can also be created, by using parentheses for
+grouping. For example, to match pages in a blog that are tagged with either
+of two tags, use:
+
+	blog/* and (tagged(foo) or tagged(bar))
+
+Note that page names in PageSpecs are matched against the absolute
+filenames of the pages in the wiki, so a pagespec "foo" used on page
+"a/b" will not match a page named "a/foo" or "a/b/foo". To match
+relative to the directory of the page containing the pagespec, you can
+use "./". For example, "./foo" on page "a/b" matches page "a/foo".
+
+To indicate the name of the page the PageSpec is used in, you can
+use a single dot. For example, `link(.)` matches all the pages
+linking to the page containing the PageSpec.
diff --git a/doc/install/Android.mdwn b/doc/install/Android.mdwn
index c39d11568..537f6d518 100644
--- a/doc/install/Android.mdwn
+++ b/doc/install/Android.mdwn
@@ -7,15 +7,20 @@ Now git-annex can be used on Android!
 First, ensure your Android device is configured to allow installation
 of the app. Go to Setup -&gt; Security, and enable "Unknown Sources".
 
-[Download the git-annex.apk](http://downloads.kitenet.net/git-annex/android/current/)
-onto your Android device, and open it to install.
+Then download the git-annex.apk for your version of Android, and 
+open it to install.
+
+* [Android 4.4 and 4.3 git-annex.apk](http://downloads.kitenet.net/git-annex/android/current/4.3/git-annex.apk)
+* [Android 4.0 to 4.2 git-annex.apk](http://downloads.kitenet.net/git-annex/android/current/4.0/git-annex.apk)
 
 ## autobuilds
 
 A daily build is also available, thanks to Mesar Hameed and the University
 of Bath CS department.
 
-* [download apk](http://downloads.kitenet.net/git-annex/autobuild/android/git-annex.apk) ([build logs](http://downloads.kitenet.net/git-annex/autobuild/android/))
+* [Android 4.4 and 4.3 git-annex.apk](http://downloads.kitenet.net/git-annex/autobuild/android/4.3/git-annex.apk)
+* [Android 4.0 to 4.2 git-annex.apk](http://downloads.kitenet.net/git-annex/autobuild/android/4.0/git-annex.apk)
+* [build logs](http://downloads.kitenet.net/git-annex/autobuild/android/)
 
 ## building it yourself
 
diff --git a/doc/install/Android/comment_13_f077a27c04131da89db1d7abcab3e68f._comment b/doc/install/Android/comment_13_f077a27c04131da89db1d7abcab3e68f._comment
deleted file mode 100644
index 4d16c171e..000000000
--- a/doc/install/Android/comment_13_f077a27c04131da89db1d7abcab3e68f._comment
+++ /dev/null
@@ -1,20 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawmK0703vNSIQsP1mGf-4MAPnsBZiSc6yVo"
- nickname="Emre"
- subject="adding ssh server"
- date="2013-10-16T16:37:10Z"
- content="""
-Thanks Joey, I will try this direct mode tonight. I'm following git-annex development since your first days, but I just decided to give it a try so bear with me :)
-
-I also have a VPS and I did try yesterday night to add it as a cloud server to make android & linux sync. It also contained git-annex. When I add it from the PC, it appeared in Android but it was not possible to use it somehow. I had to add a new cloud server with exactly the same settings like th PC, which made things complicated to understand for me as to what happens on the server side when both computers try to setup a repository. (the sync didn't work neither)
-Maybe I hit a bug here so wanted to share with you.
-What I expected is that, 
-1) Add a VPS/ssh/git-annex cloud option from PC.
-2) It shall appear in the Android webapp using the XMPP control channel
-3) if the password or private key can't be synced over the XMPP due to security concern, then the Android webapp shall just ask for the password to enable it, nothing more.
-
-2nd thing, when I add this VPS/SSH/Git-annex from the PC, if I do not choose any encryption, it is marked as \"sync enabled\". IF I choose \"shared encryption\" instead, then sync gets disabled and there's nowhere any comment why the sync is disabled. So, by trial and error, I concluded that the sync is not supported in shared encryption remotes?
-
-3rd thing: The remote cloud can be configured for example as \"full backup\" or \"transfer host\". What is not clear is that if I configure it as a \"full backup\" host, then can Android and PC still use it as a \"transfer host\" to sync between themselves? What I would expect is that once I add this cloud vps as a \"full backup\" host, then everybody syncs with it and gets a copy from it if they can't communicate directly themselves. 
-Hope I did not confuse things much, thanks a lot even if you don't find time to write answers.
-"""]]
diff --git a/doc/install/Android/comment_5_40cb6cb72c4ad4aa19a4a40f41a6a757._comment b/doc/install/Android/comment_5_40cb6cb72c4ad4aa19a4a40f41a6a757._comment
deleted file mode 100644
index 74c207306..000000000
--- a/doc/install/Android/comment_5_40cb6cb72c4ad4aa19a4a40f41a6a757._comment
+++ /dev/null
@@ -1,13 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawnljkMF1zhScDfvJYMhXXubnar_DakLoas"
- nickname="Tony"
- subject="broken under 4.3?"
- date="2013-07-28T00:36:51Z"
- content="""
-Things seem broken under the recently released 4.3 release for nexus devices:
-
->Falling back to hardcoded app location;         cannot find expected files in /data/app-lib
->u0_a33@mako:/sdcard/git-annex.home $     git annex webapp
->CANNOT LINK EXECUTABLE: git-annex     invalid R_ARM_COPY relocation against     DT_SYMBOLIC shared library libc.so (built.    with -Bsymbolic?)
->1|u0_a33@mako:/sdcard/git-annex.home $
-"""]]
diff --git a/doc/install/Android/comment_6_b0f723538e7328d5070c563f070858bd._comment b/doc/install/Android/comment_6_b0f723538e7328d5070c563f070858bd._comment
deleted file mode 100644
index e6a7aa072..000000000
--- a/doc/install/Android/comment_6_b0f723538e7328d5070c563f070858bd._comment
+++ /dev/null
@@ -1,8 +0,0 @@
-[[!comment format=mdwn
- username="justjohn"
- ip="71.233.149.123"
- subject="Broken on 4.3 on Nexus 7"
- date="2013-07-28T16:14:18Z"
- content="""
-I'm seeing the same error as the previous comment from Tony on my Nexus 7 after I updated it to the stock (albeit rooted) 4.3 release from Google.
-"""]]
diff --git a/doc/install/Android/comment_7_c6dc23d0e6f4138c4bf8e3452755676f._comment b/doc/install/Android/comment_7_c6dc23d0e6f4138c4bf8e3452755676f._comment
deleted file mode 100644
index 61c1a916b..000000000
--- a/doc/install/Android/comment_7_c6dc23d0e6f4138c4bf8e3452755676f._comment
+++ /dev/null
@@ -1,8 +0,0 @@
-[[!comment format=mdwn
- username="https://www.google.com/accounts/o8/id?id=AItOawl9sYlePmv1xK-VvjBdN-5doOa_Xw-jH4U"
- nickname="Richard"
- subject="comment 7"
- date="2013-07-30T15:02:51Z"
- content="""
-@Tony @justjohn: I created a proper bug for this: [[bugs/git-annex_broken_on_Android_4.3]]
-"""]]
diff --git a/doc/install/Debian.mdwn b/doc/install/Debian.mdwn
index 2158794b1..c71d4d244 100644
--- a/doc/install/Debian.mdwn
+++ b/doc/install/Debian.mdwn
@@ -9,6 +9,10 @@
 Note: This version does not include support for the [[assistant]].
 A backport is available with the assistant and other new features.
 
+Follow the instructions to [enable backports](http://backports.debian.org/Instructions/).
+
+	sudo apt-get -t wheezy-backports install git-annex
+
 ## Debian 6.0 "squeeze"
 
 Follow the instructions to [enable backports](http://backports.debian.org/Instructions/).
diff --git a/doc/install/OSX.mdwn b/doc/install/OSX.mdwn
index fba44e2a4..e3b15069d 100644
--- a/doc/install/OSX.mdwn
+++ b/doc/install/OSX.mdwn
@@ -1,12 +1,13 @@
 ## git-annex.app
 
 [[!img /assistant/osx-app.png align=right link=/assistant]]
-For easy installation, use the
-[beta release of git-annex.app](https://downloads.kitenet.net/git-annex/OSX/current/).
+For easy installation, use the prebuilt app bundle.
 
-Be sure to select the build matching your version of OSX.
+* 10.9 Mavericks: [git-annex.dmg](https://downloads.kitenet.net/git-annex/OSX/current/10.9_Mavericks/git-annex.dmg)
+* 10.8.2 Mountain Lion: [git-annex.dmg.bz2](https://downloads.kitenet.net/git-annex/OSX/current/10.8.2_Mountain_Lion/git-annex.dmg.bz2) **warning: not being updated any longer**
+* 10.7.5 Lion: [git-annex.dmg](https://downloads.kitenet.net/git-annex/OSX/current/10.7.5_Lion/git-annex.dmg)
 
-If you want to run the [[git-annex_assistant|/assistant]], just
+To run the [[git-annex_assistant|/assistant]], just
 install the app, look for the icon, and start it up. 
 
 To use git-annex at the command line, you can add
@@ -17,20 +18,17 @@ Alternatively, from the command line you can run
 programs bundled inside the app, including not just git-annex, but git, and
 several more. Handy if you don't otherwise have git installed.
 
-This is still a work in progress. See [[/bugs/OSX_app_issues]] for problem
-reports.
-
 ## autobuilds
 
 [Jimmy Tang](http://www.sgenomics.org/~jtang/) autobuilds
 the app for OSX Lion.
 
-* [autobuild of git-annex.app](http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/ref/master/git-annex.dmg.bz2) ([build logs](http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/))
+* [autobuild of git-annex.dmg](http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/ref/master/git-annex.dmg.bz2) ([build logs](http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/))
   * [past builds](http://www.sgenomics.org/~jtang/gitbuilder-git-annex-x00-x86_64-apple-darwin10.8.0-binary/sha1/) -- directories are named from the commitid's
 
-[[Joey]] autobuilds the app for Mountain Lion.
+[[Joey]] autobuilds the app for Mavericks.
 
-* [autobuild of git-annex.app](https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mountain-lion/git-annex.dmg.bz2) ([build logs](https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mountain-lion/))
+* [autobuild of git-annex.dmg](https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mavericks/git-annex.dmg) ([build logs](https://downloads.kitenet.net/git-annex/autobuild/x86_64-apple-mavericks/))
 
 ## using Brew
 
diff --git a/doc/install/OSX/comment_32_a46d8e3e7795b9afb1e1c2be943d12af._comment b/doc/install/OSX/comment_32_a46d8e3e7795b9afb1e1c2be943d12af._comment
index dbb0433f7..290da58f8 100644
--- a/doc/install/OSX/comment_32_a46d8e3e7795b9afb1e1c2be943d12af._comment
+++ b/doc/install/OSX/comment_32_a46d8e3e7795b9afb1e1c2be943d12af._comment
@@ -4,7 +4,7 @@
  subject="comment 32"
  date="2013-10-21T22:47:14Z"
  content="""
-You probably need to install libdbus dev stuff, and then the haskell dbus library. But it's certianly going to need code changes to make git-annex use dbus in any way on OSX, assuming there are even useful dbus events generated for network connections and drives being mounted on OSX.
+You probably need to install libdbus dev stuff, and then the haskell dbus library. But it's certainly going to need code changes to make git-annex use dbus in any way on OSX, assuming there are even useful dbus events generated for network connections and drives being mounted on OSX.
 
 It was saying \"gcrypt\" when it meant \"git-remote-gcrypt\".
 """]]
diff --git a/doc/install/Ubuntu.mdwn b/doc/install/Ubuntu.mdwn
index 107a1a8e7..61b1489ff 100644
--- a/doc/install/Ubuntu.mdwn
+++ b/doc/install/Ubuntu.mdwn
@@ -1,7 +1,17 @@
-## Saucy, Raring
+## Saucy
 
 	sudo apt-get install git-annex
 
+Warning: The version of git-annex shipped in Ubuntu Saucy had
+[a bug that can cause problems when creating repositories using the webapp](http://git-annex.branchable.com/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__/).
+
+## Raring
+	
+	sudo apt-get install git-annex
+
+Note: This version is too old to include the [[assistant]] or its WebApp,
+but is otherwise usable.
+
 ## Precise
 
 	sudo apt-get install git-annex
diff --git a/doc/install/Ubuntu/comment_12_38f69dffe2db0d15e4c4e5cb47f40ef8._comment b/doc/install/Ubuntu/comment_12_38f69dffe2db0d15e4c4e5cb47f40ef8._comment
new file mode 100644
index 000000000..7cbf8c0ae
--- /dev/null
+++ b/doc/install/Ubuntu/comment_12_38f69dffe2db0d15e4c4e5cb47f40ef8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="Raring?"
+ date="2013-11-01T20:28:04Z"
+ content="""
+I'm also on Raring and the latest version available is 3.20121112ubuntu4, nearly a year old.  The PPA is only for Precise.  The tarball is a daily snapshot, and I would much rather run a released version right now.  What can I do?  Can't the PPA be built automatically for Raring and Saucy?
+"""]]
diff --git a/doc/install/cabal.mdwn b/doc/install/cabal.mdwn
index 4eac597f1..3270dd0f9 100644
--- a/doc/install/cabal.mdwn
+++ b/doc/install/cabal.mdwn
@@ -50,3 +50,9 @@ you want, and use cabal as follows inside its source tree:
 	cabal configure
 	cabal build
 	cabal install --bindir=$HOME/bin
+
+## EKG
+
+When building with cabal, you can optionally enable the 
+[[EKG monitoring interface|ekg]]. This is great for debugging resource
+usage problems.
diff --git a/doc/install/cabal/comment_26_bd455c732639728bce2bfc39e32871d2._comment b/doc/install/cabal/comment_26_bd455c732639728bce2bfc39e32871d2._comment
new file mode 100644
index 000000000..5b1f06023
--- /dev/null
+++ b/doc/install/cabal/comment_26_bd455c732639728bce2bfc39e32871d2._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 26"
+ date="2013-11-01T16:33:25Z"
+ content="""
+@RaspberryPie that only affected builds without the webapp, in any case it's fixed now.
+"""]]
diff --git a/doc/install/cabal/comment_27_c080e9239b6eec88d329c28da7bb4141._comment b/doc/install/cabal/comment_27_c080e9239b6eec88d329c28da7bb4141._comment
new file mode 100644
index 000000000..4c007c9ad
--- /dev/null
+++ b/doc/install/cabal/comment_27_c080e9239b6eec88d329c28da7bb4141._comment
@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="RaspberryPie"
+ ip="37.221.160.203"
+ subject="comment 27"
+ date="2013-11-02T12:52:18Z"
+ content="""
+Okay, the error doesn't show up anymore. I didn't even get to Cronner though, because this time I got a different error:
+
+    Assistant/Alert.hs:195:20:
+        Couldn't match expected type `Assistant ()' with actual type `()'
+        Expected type: Maybe Remote -> Assistant ()
+          Actual type: Maybe Remote -> ()
+        In the expression: noop
+        In an equation for `notFsckedNudge': notFsckedNudge _ = noop
+
+This is from trying to compile 4.20131101 with `-f\"-webapp -webdav\"`
+"""]]
diff --git a/doc/install/cabal/comment_28_15951dd070a675300420eea137a28ef9._comment b/doc/install/cabal/comment_28_15951dd070a675300420eea137a28ef9._comment
new file mode 100644
index 000000000..19a570cae
--- /dev/null
+++ b/doc/install/cabal/comment_28_15951dd070a675300420eea137a28ef9._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 28"
+ date="2013-11-02T17:40:18Z"
+ content="""
+Unfortunate about that. I've fixed it in git.
+
+(It would be best to file bug reports about build failures to avoid cluttering up this page.)
+"""]]
diff --git a/doc/install/cabal/comment_29_ac082dca67f4a29b06070c0283130f52._comment b/doc/install/cabal/comment_29_ac082dca67f4a29b06070c0283130f52._comment
new file mode 100644
index 000000000..524a0db0c
--- /dev/null
+++ b/doc/install/cabal/comment_29_ac082dca67f4a29b06070c0283130f52._comment
@@ -0,0 +1,39 @@
+[[!comment format=mdwn
+ username="robohack"
+ ip="24.67.98.78"
+ subject="cabal install failing due to problems building pcre-light-0.4"
+ date="2013-11-21T20:17:10Z"
+ content="""
+After a fresh install of Haskell, and following the instructions above, I end up with the following rather bizarre and unexpected problem:
+
+	$ cabal install git-annex --bindir=$HOME/bin -f\"-assistant -webapp -webdav -pairing -xmpp -dns\"
+	Resolving dependencies...
+	Configuring pcre-light-0.4...
+	Building pcre-light-0.4...
+	Preprocessing library pcre-light-0.4...
+	Base.hsc:103:18: error: pcre.h: No such file or directory
+	Base.hsc: In function ‘main’:
+	Base.hsc:402: error: ‘PCRE_ANCHORED’ undeclared (first use in this function)
+	Base.hsc:402: error: (Each undeclared identifier is reported only once
+	Base.hsc:402: error: for each function it appears in.)
+	Base.hsc:405: error: ‘PCRE_AUTO_CALLOUT’ undeclared (first use in this function)
+
+(followed by an error for every other macro that was expected to be defined in the header...)
+
+	compiling dist/build/Text/Regex/PCRE/Light/Base_hsc_make.c failed (exit code 1)
+	command was: /usr/bin/gcc -c dist/build/Text/Regex/PCRE/Light/Base_hsc_make.c -o dist/build/Text/Regex/PCRE/Light/Base_hsc_make.o -m64 -fno-stack-protector -m64 -fno-stack-protector -m64 -D__GLASGOW_HASKELL__=700 -Ddarwin_BUILD_OS -Ddarwin_HOST_OS -Dx86_64_BUILD_ARCH -Dx86_64_HOST_ARCH -I/sw/lib/ghc-7.0.4/bytestring-0.9.1.10/include -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -I/sw/lib/ghc-7.0.4/base-4.3.1.0/include -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -I/sw/lib/ghc-7.0.4/include -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -I/sw/lib/ghc-7.0.4/include -Idist/build/autogen -include dist/build/autogen/cabal_macros.h -I/sw/lib/ghc-7.0.4/include/
+	Failed to install pcre-light-0.4
+	cabal: Error: some packages failed to install:
+	git-annex-3.20120230 depends on pcre-light-0.4 which failed to install.
+	pcre-light-0.4 failed during the building phase. The exception was:
+	ExitFailure 1
+
+This is a somewhat older Mac OS X 10.6.8 system.
+
+I do have PCRE already installed via Fink, and pcre.h is in /sw/include.  I see other -I/sw/... things in the compile command above, but obviously /sw/include is not one of them.
+
+Any clues for me?
+
+(Why the heck does git-annex need pcre in particular anyway???  I saw another regex library get installed earlier somewhere in this (massive) process.)
+
+"""]]
diff --git a/doc/install/cabal/comment_30_ad639c07cb79e89406e95c1dafce3a01._comment b/doc/install/cabal/comment_30_ad639c07cb79e89406e95c1dafce3a01._comment
new file mode 100644
index 000000000..f068944b0
--- /dev/null
+++ b/doc/install/cabal/comment_30_ad639c07cb79e89406e95c1dafce3a01._comment
@@ -0,0 +1,35 @@
+[[!comment format=mdwn
+ username="robohack"
+ ip="24.67.98.78"
+ subject="hmmm... ok, the PCRE problem was odd, but now this:"
+ date="2013-11-21T20:30:54Z"
+ content="""
+The PCRE problem is solved trivially in my case with a couple more cabal install options, though the need for these seems oddly dissatisfying given the reams of other stuff that was successfully built and installed without these options.
+
+Now however I seem to have encountered a deeper problem:
+
+	$ cabal install git-annex --bindir=$HOME/bin --extra-include-dirs=/sw/include --extra-lib-dirs=/sw/lib               
+	Resolving dependencies...
+	[1 of 1] Compiling Main             ( /var/folders/7h/7hWHR5m8HPKOnUEvQU7HU++++TI/-Tmp-/git-annex-3.20120230-84797/git-annex-3.20120230/Setup.hs, /var/folders/7h/7hWHR5m8HPKOnUEvQU7HU++++TI/-Tmp-/git-annex-3.20120230-84797/git-annex-3.20120230/dist/setup/Main.o )
+	Linking /var/folders/7h/7hWHR5m8HPKOnUEvQU7HU++++TI/-Tmp-/git-annex-3.20120230-84797/git-annex-3.20120230/dist/setup/setup ...
+	hsc2hs Utility/StatFS.hsc
+	perl -i -pe 's/^{-# INCLUDE.*//' Utility/StatFS.hs
+	ghc -O2 -Wall -ignore-package monads-fd --make configure
+	
+	Utility/StatFS.hsc:54:8:
+	    Could not find module `GHC.Foreign':
+	      Use -v to see a list of the files searched for.
+	make: *** [Build/SysConfig.hs] Error 1
+	Configuring git-annex-3.20120230...
+	Building git-annex-3.20120230...
+	Preprocessing executable 'git-annex' for git-annex-3.20120230...
+	
+	Git/Version.hs:11:18:
+	    Could not find module `Build.SysConfig':
+	      Use -v to see a list of the files searched for.
+	Failed to install git-annex-3.20120230
+	cabal: Error: some packages failed to install:
+	git-annex-3.20120230 failed during the building phase. The exception was:
+	ExitFailure 1
+
+"""]]
diff --git a/doc/install/cabal/comment_31_4763b24a29627d55f465b9ea260ea7ec._comment b/doc/install/cabal/comment_31_4763b24a29627d55f465b9ea260ea7ec._comment
new file mode 100644
index 000000000..224c1dc19
--- /dev/null
+++ b/doc/install/cabal/comment_31_4763b24a29627d55f465b9ea260ea7ec._comment
@@ -0,0 +1,22 @@
+[[!comment format=mdwn
+ username="robohack"
+ ip="24.67.98.78"
+ subject="a different error trying to build from the git repo...."
+ date="2013-11-21T21:14:54Z"
+ content="""
+I'm using the ghc7.0 branch because Fink's GHC is still at 7.0.4....
+
+	$ cabal build                                
+	Building git-annex-3.20120523...
+	Preprocessing executable 'git-annex' for git-annex-3.20120523...
+	[ 78 of 163] Compiling Utility.Url      ( Utility/Url.hs, dist/build/git-annex/git-annex-tmp/Utility/Url.o )
+	
+	Utility/Url.hs:111:88:
+	    Couldn't match expected type `Maybe URI' with actual type `URI'
+	    In the second argument of `fromMaybe', namely
+	      `(newURI `relativeTo` u)'
+	    In the expression: fromMaybe newURI (newURI `relativeTo` u)
+	    In an equation for `newURI_abs':
+	        newURI_abs = fromMaybe newURI (newURI `relativeTo` u)
+
+"""]]
diff --git a/doc/install/cabal/comment_32_1d34c294486c85b1149675fa5861ae35._comment b/doc/install/cabal/comment_32_1d34c294486c85b1149675fa5861ae35._comment
new file mode 100644
index 000000000..8b2ae67f9
--- /dev/null
+++ b/doc/install/cabal/comment_32_1d34c294486c85b1149675fa5861ae35._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 32"
+ date="2013-11-22T16:27:36Z"
+ content="""
+@robohack, the ghc7.0 branch is not being maintained, and is so old I don't recommend it. To build it against current cabal you will probably need to version its dependency on network to an older version than 2.4.0. 
+
+Also, git-annex has not depended on pcre for a long time. But you're building thoroughly old version so get to trip over every bug that's been reported for the past 2 years..
+"""]]
diff --git a/doc/internals.mdwn b/doc/internals.mdwn
index 84d9bcb50..4665d38df 100644
--- a/doc/internals.mdwn
+++ b/doc/internals.mdwn
@@ -16,7 +16,7 @@ Each subdirectory has the [[name_of_a_key|key_format]] in one of the
 [[key-value_backends|backends]]. The file inside also has the name of the key.
 This two-level structure is used because it allows the write bit to be removed
 from the subdirectories as well as from the files. That prevents accidentially
-deleting or changing the file contents.
+deleting or changing the file contents. See [[lockdown]] for details.
 
 In [[direct_mode]], file contents are not stored in here, and instead
 are stored directly in the file. However, the same symlinks are still
diff --git a/doc/internals/comment_1_4b8ed353dca4f484b3b6eb463fa02fd8._comment b/doc/internals/comment_1_4b8ed353dca4f484b3b6eb463fa02fd8._comment
new file mode 100644
index 000000000..b42cd2fd8
--- /dev/null
+++ b/doc/internals/comment_1_4b8ed353dca4f484b3b6eb463fa02fd8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="stoile"
+ ip="2a01:198:242:0:219:66ff:fef2:c021"
+ subject="tmp missing"
+ date="2013-11-16T12:16:48Z"
+ content="""
+There's no information about .git/annex/tmp here.
+"""]]
diff --git a/doc/internals/comment_2_c19232d5cc4976c2e5b014aef6e8d9ec._comment b/doc/internals/comment_2_c19232d5cc4976c2e5b014aef6e8d9ec._comment
new file mode 100644
index 000000000..3c5f87bd5
--- /dev/null
+++ b/doc/internals/comment_2_c19232d5cc4976c2e5b014aef6e8d9ec._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 2"
+ date="2013-11-16T17:23:02Z"
+ content="""
+.git/annex/tmp is not very interesting. It's a temporary file directory. When transferring a key's content, git-annex uses a stable filename, which allows resuming interrupted downloads, or cleaning up aborted downloads with `git annex unused`.
+"""]]
diff --git a/doc/internals/lockdown.mdwn b/doc/internals/lockdown.mdwn
new file mode 100644
index 000000000..a7775cd3a
--- /dev/null
+++ b/doc/internals/lockdown.mdwn
@@ -0,0 +1,44 @@
+Object files stored in `.git/annex/objects` are each put in their own directory.
+This allows the write bit to be removed from both the file, and its directory,
+which prevents accidentially deleting or changing the file contents.
+
+The reasoning for doing this follows:
+
+Normally with git, once you have committed a file, editing the file in the
+working tree cannot cause you to lose the committed version. This is an
+important property of git. Of course you can `rm -rf .git` and delete
+commits if you like (before you've pushed them). But you can't lose a
+committed version of the file because of something you do with the working
+tree version.
+
+It's easy for git to do this, because committing a file makes a copy of it.
+But git-annex does not make a local copy of a file added to it, because
+the file could be very large.
+
+So, it's important for git-annex to find another way to preserve the expected
+property that once committed, you cannot accidentially lose a file.
+The most important protection it makes is just to remove the write bit of
+the file. Thus preventing programs from modifying it.
+
+But, that does not prevent any program that might follow the symlink and
+delete the symlinked file. This might seem an unlikely thing for a program to
+do at first, but consider a command like:
+`tar cf foo.tar foo --remove-files --dereference`
+
+When I tested this, I didn't know if it would remove the file foo symlinked
+to or not! It turned out that my tar doesn't remove it. But it could
+have easily went the other way.
+
+Rather than needing to worry about every possible program that might
+decide to do something like this, git-annex removes the write bit from the
+directory containing the annexed object, as well as removing the write
+bit from the file. (The only bad consequence of this is that `rm -rf .git`
+doesn't work unless you first run `chmod -R +w .git`)
+
+----
+
+It's known that this lockdown mechanism is incomplete. The worst hole in
+it is that if you explicitly run `chmod +w` on an annexed file in the working
+tree, this follows the symlink and allows writing to the file. It would be
+better to make the files fully immutable. But most systems either don't
+support immutable attributes, or only let root make files immutable.
diff --git a/doc/news/2013_git-annex_user_survey.mdwn b/doc/news/2013_git-annex_user_survey.mdwn
new file mode 100644
index 000000000..269496e64
--- /dev/null
+++ b/doc/news/2013_git-annex_user_survey.mdwn
@@ -0,0 +1,5 @@
+Similar to the yearly git user survey, I am doing a
+[2013 git-annex user survey](http://git-annex-survey.branchable.com/polls/2013/).
+
+If you use git-annex,
+please take a few minutes to answer my questions!
diff --git a/doc/news/version_4.20130827.mdwn b/doc/news/version_4.20130827.mdwn
deleted file mode 100644
index 767e912fe..000000000
--- a/doc/news/version_4.20130827.mdwn
+++ /dev/null
@@ -1,27 +0,0 @@
-git-annex 4.20130827 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * Youtube support! (And 53 other video hosts). When quvi is installed,
-     git-annex addurl automatically uses it to detect when an page is
-     a video, and downloads the video file.
-   * web special remote: Also support using quvi, for getting files,
-     or checking if files exist in the web.
-   * unused: Is now a minimum of 30 times faster, and typically many
-     more times than that (when a repository has several branches).
-     (Thanks, guilhem for the patch.)
-   * unused: Fix bugs in two edge cases involving manually staged changes.
-     (Thanks, guilhem for the patch.)
-   * Android: Fix bug in terminal app that caused it to spin using much
-     CPU and battery. This problem was introduced in version 4.20130601.
-   * sync, merge: Bug fix: Don't try to merge into master when in a bare repo.
-   * import: Add options to control handling of duplicate files:
-     --duplicate, --deduplicate, and --clean-duplicates
-   * mirror: New command, makes two repositories contain the same set of files.
-   * Set --clobber when running wget to ensure resuming works properly.
-   * Unescape characters in 'file://...' URIs. (Thanks, guilhem for the patch.)
-   * Better error message when trying to use a git remote that has annex.ignore
-     set.
-   * Fix bug that caused typechanged symlinks to be assumed to be unlocked
-     files, so they were added to the annex by the pre-commit hook.
-   * Debian: Run the builtin test suite as an autopkgtest.
-   * Debian: Recommend ssh-askpass, which ssh will use when the assistant
-     is run w/o a tty. Closes: #[719832](http://bugs.debian.org/719832)"""]]
\ No newline at end of file
diff --git a/doc/news/version_4.20130909.mdwn b/doc/news/version_4.20130909.mdwn
deleted file mode 100644
index ead359898..000000000
--- a/doc/news/version_4.20130909.mdwn
+++ /dev/null
@@ -1,36 +0,0 @@
-git-annex 4.20130909 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * initremote: Syntax change when setting up an encrypted special remote.
-     Now use keyid=$KEYID rather than the old encryption=$KEYID
-   * forget: New command, causes git-annex branch history to be forgotten
-     in a way that will spread to other clones of the repository.
-     (As long as they're running this version or newer of git-annex.)
-   * forget --drop-dead: Completely removes mentions of repositories that
-     have been marked as dead from the git-annex branch.
-   * sync, assistant: Force push of the git-annex branch. Necessary
-     to ensure it gets pushed to remotes after being rewritten by forget.
-   * Added gcrypt support. This combines a fully encrypted git
-     repository (using git-remote-gcrypt) with an encrypted git-annex special
-     remote.
-   * sync: Support syncing with gcrypt remotes.
-   * importfeed: Also ignore transient problems with downloading content
-     from feeds.
-   * Honor core.sharedrepository when receiving and adding files in direct
-     mode.
-   * enableremote: gpg keys can be removed from those a remote encrypts
-     to by passing "keyid-=$KEYID". keyid+= is also provided.
-     (Thanks, guilhem for the patch.)
-   * Added encryption=pubkey scheme, which encrypts to public keys directly
-     rather than the hybrid approach. See documentation for advantages
-     and disadvantages, but encryption=hybrid is the recommended scheme still.
-     (Thanks, guilhem for the patch.)
-   * Fix Feeds display in build flags.
-   * Remind user when annex-ignore is set for some remotes, if unable to
-     get or drop a file, possibly because it's on an ignored remote.
-   * gpg: Force --no-textmode in case the user has it turned on in config.
-   * webapp: Improve javascript's handling of longpolling connection
-     failures, by reloading the current page in this case.
-     Works around chromium behavior where ajax connections to urls
-     that were already accessed are denied after navigating back to
-     a previous page.
-   * Allow building without quvi support."""]]
\ No newline at end of file
diff --git a/doc/news/version_4.20131002.mdwn b/doc/news/version_4.20131002.mdwn
deleted file mode 100644
index 90692e4f2..000000000
--- a/doc/news/version_4.20131002.mdwn
+++ /dev/null
@@ -1,42 +0,0 @@
-News for git-annex 4.20131002:
-
-    The layout of gcrypt repositories has changed, and
-    if you created one you must manually upgrade it.
-    See /usr/share/doc/git-annex/html/upgrades/gcrypt.html
-
-git-annex 4.20131002 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * Note that the layout of gcrypt repositories has changed, and
-     if you created one you must manually upgrade it.
-     See http://git-annex.branchable.com/upgrades/gcrypt/
-   * webapp: Support setting up and using encrypted git repositories on
-     any ssh server, as well as on rsync.net.
-   * git-annex-shell: Added support for operating inside gcrypt repositories.
-   * Disable receive.denyNonFastForwards when setting up a gcrypt special
-     remote, since gcrypt needs to be able to fast-forward the master branch.
-   * import: Preserve top-level directory structure.
-   * Use cryptohash rather than SHA for hashing when no external hash program
-     is available. This is a significant speedup for SHA256 on OSX, for
-     example.
-   * Added SKEIN256 and SKEIN512 backends.
-   * Android build redone from scratch, many dependencies updated,
-     and entire build can now be done using provided scripts.
-   * assistant: Clear the list of failed transfers when doing a full transfer
-     scan. This prevents repeated retries to download files that are not
-     available, or are not referenced by the current git tree.
-   * indirect, direct: Better behavior when a file is not owned by
-     the user running the conversion.
-   * add, import, assistant: Better preserve the mtime of symlinks,
-     when when adding content that gets deduplicated.
-   * Send a git-annex user-agent when downloading urls.
-     Overridable with --user-agent option.
-     (Not yet done for S3 or WebDAV due to limitations of libraries used.)
-   * webapp: Fixed a bug where when a new remote is added, one file
-     may fail to sync to or from it due to the transferrer process not
-     yet knowing about the new remote.
-   * OSX: Bundled gpg upgraded, now compatible with config files
-     written by MacGPG.
-   * assistant: More robust inotify handling; avoid crashing if a directory
-     cannot be read.
-   * Moved list of backends and remote types from status to version
-     command."""]]
\ No newline at end of file
diff --git a/doc/news/version_4.20131101.mdwn b/doc/news/version_4.20131101.mdwn
new file mode 100644
index 000000000..2c6bb309d
--- /dev/null
+++ b/doc/news/version_4.20131101.mdwn
@@ -0,0 +1,29 @@
+git-annex 4.20131101 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * The "git annex content" command is renamed to "git annex wanted".
+   * New --want-get and --want-drop options which can be used to
+     test preferred content settings.
+     For example, "git annex find --in . --want-drop"
+   * assistant: When autostarted, wait 5 seconds before running the startup
+     scan, to avoid contending with the user's desktop login process.
+   * webapp: When setting up a bare shared repository, enable non-fast-forward
+     pushes.
+   * sync: Show a hint about receive.denyNonFastForwards when a push fails.
+   * directory, webdav: Fix bug introduced in version 4.20131002 that
+     caused the chunkcount file to not be written. Work around repositories
+     without such a file, so files can still be retreived from them.
+   * assistant: Automatically repair damanged git repository, if it can
+     be done without losing data.
+   * assistant: Support repairing git remotes that are locally accessible
+     (eg, on removable drives).
+   * add: Fix reversion in 4.20130827 when adding unlocked files that have
+     not yet been committed.
+   * unannex: New, much slower, but more safe behavior: Copies files out of
+     the annex. This avoids an unannex of one file breaking other files that
+     link to the same content. Also, it means that the content
+     remains in the annex using up space until cleaned up with
+     "git annex unused".
+     (The behavior of unannex --fast has not changed; it still hard links
+     to content in the annex. --fast was not made the default because it is
+     potentially unsafe; editing such a hard linked file can unexpectedly
+     change content stored in the annex.)"""]]
\ No newline at end of file
diff --git a/doc/news/version_4.20131106.mdwn b/doc/news/version_4.20131106.mdwn
new file mode 100644
index 000000000..061d02100
--- /dev/null
+++ b/doc/news/version_4.20131106.mdwn
@@ -0,0 +1,18 @@
+git-annex 4.20131106 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * Improve local pairing behavior when two computers both try to start
+     the pairing process separately.
+   * sync: Work even when the local git repository is new and empty,
+     with no master branch.
+   * gcrypt, bup: Fix bug that prevented using these special remotes
+     with encryption=pubkey.
+   * Fix enabling of gcrypt repository accessed over ssh;
+     git-annex-shell gcryptsetup had a bug that caused it to fail
+     with permission denied.
+   * Fix zombie process that occurred when switching between repository
+     views in the webapp.
+   * map: Work when there are gcrypt remotes.
+   * Fix build w/o webapp.
+   * Fix exception handling bug that could cause .git/annex/index to be used
+     for git commits outside the git-annex branch. Known to affect git-annex
+     when used with the git shipped with Ubuntu 13.10."""]]
\ No newline at end of file
diff --git a/doc/news/version_5.20131118.mdwn b/doc/news/version_5.20131118.mdwn
new file mode 100644
index 000000000..2323ec63b
--- /dev/null
+++ b/doc/news/version_5.20131118.mdwn
@@ -0,0 +1,42 @@
+git-annex 5.20131118 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * Direct mode repositories now have core.bare=true set, to prevent
+     accidentally running git commands that try to operate on the work tree,
+     and so do the wrong thing in direct mode.
+   * annex.version is now set to 5 for direct mode repositories.
+     This upgrade is handled fully automatically, no need to run
+     git annex upgrade
+   * The "status" command has been renamed to "info", to allow
+     "git annex status" to be used in direct mode repositories, now that
+     "git status" won't work in them.
+   * The -c option now not only modifies the git configuration seen by
+     git-annex, but it is passed along to every git command git-annex runs.
+   * watcher: Avoid loop when adding a file owned by someone else fails
+     in indirect mode because its permissions cannot be modified.
+   * webapp: Avoid encoding problems when displaying the daemon log file.
+   * webapp: Improve UI around remote that have no annex.uuid set,
+     either because setup of them is incomplete, or because the remote
+     git repository is not a git-annex repository.
+   * Include ssh-keygen in standalone bundle.
+   * Allow optionally configuring git-annex with -fEKG to enable awesome
+     remote monitoring interfaceat http://localhost:4242/
+   * Fix bug that caused bad information to be written to the git-annex branch
+     when running describe or other commands with a remote that has no uuid.
+   * Work around Android linker problem that had prevented git-annex from
+     running on Android 4.3 and 4.4.
+   * repair: Handle case where index file is corrupt, but all objects are ok.
+   * assistant: Notice on startup when the index file is corrupt, and
+     auto-repair.
+   * Fix direct mode merge bug when a direct mode file was deleted and replaced
+     with a directory. An ordering problem caused the directory to not get
+     created in this case.
+     Thanks to Tim for the test case.
+   * Direct mode .git/annex/objects directories are no longer left writable,
+     because that allowed writing to symlinks of files that are not present,
+     which followed the link and put bad content in an object location.
+     Thanks to Tim for the test case.
+   * fsck: Fix up .git/annex/object directory permissions.
+   * Switched to the tasty test framework.
+   * Android: Adjust default .gitignore to ignore .thumbnails at any location
+     in the tree, not just at its top.
+   * webapp: Check annex.version."""]]
\ No newline at end of file
diff --git a/doc/news/version_5.20131120.mdwn b/doc/news/version_5.20131120.mdwn
new file mode 100644
index 000000000..0470e3336
--- /dev/null
+++ b/doc/news/version_5.20131120.mdwn
@@ -0,0 +1,11 @@
+git-annex 5.20131120 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * Fix Debian package to not try to run test suite, since haskell-tasty
+     is not out of new or in Build-Depends yet.
+   * dropunused, addunused: Allow "all" instead of a range to
+     act on all unused data.
+   * Ensure execute bit is set on directories when core.sharedrepository is set.
+   * Ensure that core.sharedrepository is honored when creating the .git/annex
+     directory.
+   * Improve repair code in the case where the index file is corrupt,
+     and this hides other problems from git fsck."""]]
\ No newline at end of file
diff --git a/doc/polls.mdwn b/doc/polls.mdwn
new file mode 100644
index 000000000..55c779867
--- /dev/null
+++ b/doc/polls.mdwn
@@ -0,0 +1,2 @@
+* [[2013 git-annex user survey|2013]]
+* [[old polls|design/assistant/polls]]
diff --git a/doc/polls/2013.mdwn b/doc/polls/2013.mdwn
new file mode 100644
index 000000000..bda584d64
--- /dev/null
+++ b/doc/polls/2013.mdwn
@@ -0,0 +1,5 @@
+This has moved to a separate site due to load issues.
+
+<http://git-annex-survey.branchable.com/polls/2013/>
+
+Any votes you made here were carried over, so no need to vote twice!
diff --git a/doc/shortcuts.mdwn b/doc/shortcuts.mdwn
new file mode 100644
index 000000000..d0f647a64
--- /dev/null
+++ b/doc/shortcuts.mdwn
@@ -0,0 +1,12 @@
+[[!if test="enabled(shortcut)"
+     then="This wiki has shortcuts **enabled**."
+     else="This wiki has shortcuts **disabled**."]]
+
+This page controls what shortcut links the wiki supports.
+
+* [[!shortcut name=debbug url="http://bugs.debian.org/%S" desc="Debian bug #%s"]]
+* [[!shortcut name=iki url="http://ikiwiki.info/%S/"]]
+* [[!shortcut name=rfc url="https://www.ietf.org/rfc/rfc%s.txt" desc="RFC %s"]]
+* [[!shortcut name=cve url="https://cve.mitre.org/cgi-bin/cvename.cgi?name=%s"]]
+* [[!shortcut name=hackage url="http://hackage.haskell.org/package/%s"]]
+* [[!shortcut name=commit url="http://source.git-annex.branchable.com/?p=source.git;a=commitdiff;h=%s"]]
diff --git a/doc/special_remotes/comment_20_6b7242721f2f2c77b634568cb737e3e3._comment b/doc/special_remotes/comment_20_6b7242721f2f2c77b634568cb737e3e3._comment
new file mode 100644
index 000000000..b17896a68
--- /dev/null
+++ b/doc/special_remotes/comment_20_6b7242721f2f2c77b634568cb737e3e3._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnWvnTWY6LrcPB4BzYEBn5mRTpNhg5EtEg"
+ nickname="Bence"
+ subject="Testing a special remote"
+ date="2013-11-24T08:24:36Z"
+ content="""
+Is there a unit test or integration test to check for the behavior of a special remote implementation and/or validity?
+
+I don't speak Haskell, so maybe there are some in the source but maybe I wouldn't recognize, so I haven't checked. If there are any tests how should I use it?
+
+Thank you,
+Bence
+"""]]
diff --git a/doc/special_remotes/comment_21_5c11e69c28b9ed4cbe238a36c0839a47._comment b/doc/special_remotes/comment_21_5c11e69c28b9ed4cbe238a36c0839a47._comment
new file mode 100644
index 000000000..1645e03e6
--- /dev/null
+++ b/doc/special_remotes/comment_21_5c11e69c28b9ed4cbe238a36c0839a47._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 21"
+ date="2013-11-24T15:58:30Z"
+ content="""
+@Bence the closest I have is some tests of particular special remotes inside Test.hs. The shell equivilant of that code is:
+
+[[!format sh \"\"\"
+set -e
+git annex copy file --to remote # tests store
+git annex drop file # tests checkpresent when remote has file
+git annex move file --from remote # tests retrieve and remove
+\"\"\"]]
+"""]]
diff --git a/doc/special_remotes/gcrypt.mdwn b/doc/special_remotes/gcrypt.mdwn
index f83a953c1..ac98c43bb 100644
--- a/doc/special_remotes/gcrypt.mdwn
+++ b/doc/special_remotes/gcrypt.mdwn
@@ -1,4 +1,4 @@
-[git-remote-gcrypt](https://github.com/blake2-ppc/git-remote-gcrypt/)
+[git-remote-gcrypt](https://github.com/joeyh/git-remote-gcrypt/)
 adds support for encrypted remotes to git. The git-annex gcrypt special
 remote allows git-annex to also store its files in such repositories.
 Naturally, git-annex encrypts the files it stores too, so everything
diff --git a/doc/special_remotes/glacier/comment_6_adb1db354dc4941e4b004e4ba34660d7._comment b/doc/special_remotes/glacier/comment_6_adb1db354dc4941e4b004e4ba34660d7._comment
new file mode 100644
index 000000000..717060fcb
--- /dev/null
+++ b/doc/special_remotes/glacier/comment_6_adb1db354dc4941e4b004e4ba34660d7._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZgZuUhZlHpd_AbbcixY0QQiutb2I7GWY"
+ nickname="Jimmy"
+ subject="I know this thread is old but..."
+ date="2013-11-18T00:27:50Z"
+ content="""
+It's working well for me, though I seem to sometimes still hit the duplicate bug listed above.
+"""]]
diff --git a/doc/special_remotes/glacier/comment_7_747e403aac5acaba00e220931e926951._comment b/doc/special_remotes/glacier/comment_7_747e403aac5acaba00e220931e926951._comment
new file mode 100644
index 000000000..045fb6041
--- /dev/null
+++ b/doc/special_remotes/glacier/comment_7_747e403aac5acaba00e220931e926951._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlq4ClC5EMN1Vq1DpWXAqP5TiDnCK1mSfk"
+ nickname="Jonas"
+ subject="Expected cost for a repository"
+ date="2013-11-24T22:32:16Z"
+ content="""
+Is there a way to estimate the cost of storing a repo on glacier?
+
+I'm especially worried because of the cost of STORE and RETRIEVE requests; there are hundreds of thousands of small files in my annex repo, so that request cost could easily dominate storage cost. Does the glacier remote do anything to minimize the number of objects stored in glacier?
+"""]]
diff --git a/doc/special_remotes/xmpp.mdwn b/doc/special_remotes/xmpp.mdwn
index 33fa1a081..86f6a7c0b 100644
--- a/doc/special_remotes/xmpp.mdwn
+++ b/doc/special_remotes/xmpp.mdwn
@@ -24,7 +24,7 @@ command line.
 ## XMPP server support status
 [[!table  data="""
 Provider|Status|Type|Notes
-[[Gmail|http://gmail.com]]|Working|?|Google apps users will have to configure `.git/annex/creds/xmpp` manually
+[[Gmail|http://gmail.com]]|Working|?|Google Apps: [setup your SRV records](http://www.olark.com/gtalk/check_srv) or configure `.git/annex/creds/xmpp` manually
 [[Coderollers|http://www.coderollers.com/xmpp-server/]]|Working|[[Openfire|http://www.igniterealtime.org/projects/openfire/]]
 [[jabber.me|http://jabber.me/]]|Working|[[Tigase|http://www.tigase.org/]]
 [[xmpp.ru.net|https://www.xmpp.ru.net]]|Working|[[jabberd2|http://jabberd2.org/]]
diff --git a/doc/special_remotes/xmpp/comment_10_c7c2e2e81cb5b2b9a5272430c835dd39._comment b/doc/special_remotes/xmpp/comment_10_c7c2e2e81cb5b2b9a5272430c835dd39._comment
new file mode 100644
index 000000000..0380af359
--- /dev/null
+++ b/doc/special_remotes/xmpp/comment_10_c7c2e2e81cb5b2b9a5272430c835dd39._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmZilYULa6CDEGfuagoDlesyakBgnf-dF8"
+ nickname="Maarten"
+ subject="Google Apps & SRV"
+ date="2013-11-27T18:13:18Z"
+ content="""
+To make XMPP via a Google Apps account work out of the box, all you need to do is add the correct SRV records to your domain's DNS zone.  If you do, you don't need to manually create creds/xmpp, you can just use the web interface, enter your full apps email address and password (remember, if 2-factor, this needs to be an application-specific password).
+
+To create the correct SRV records (and check whether they're correct), see http://www.olark.com/gtalk/check_srv
+"""]]
diff --git a/doc/special_remotes/xmpp/comment_9_eda76b826491c96b1ce072aacf9d3adf._comment b/doc/special_remotes/xmpp/comment_9_eda76b826491c96b1ce072aacf9d3adf._comment
new file mode 100644
index 000000000..3505f3aaf
--- /dev/null
+++ b/doc/special_remotes/xmpp/comment_9_eda76b826491c96b1ce072aacf9d3adf._comment
@@ -0,0 +1,23 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawlu-fdXIt_RF9ggvg4zP0yBbtjWQwHAMS4"
+ nickname="Jörn"
+ subject="Same problem, no XMPP showing up in daemon.log"
+ date="2013-11-21T21:13:16Z"
+ content="""
+I have the same setup like @RaspberryPie, except that my server is not running on the Pi but on Debian7-amd64. On my client (OSX, self-compiled using cabal) I can see XMPP log entries like @RaspberryPi, however, on the Debian7 machine (also self-compiled) I do not see any XMPP entry in the daemon.log. Setup regarding .git/annex/creds/xmpp and the special xmpp remote is correct (checked a thousand times).
+
+Do you have any idea what could be wrong, Joey? Thanks a lot.
+
+Output of git annex version:
+
+    git-annex version: 5.20131120
+    build flags: Assistant Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi CryptoHash 
+    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
+    remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
+    local repository version: 4
+    default repository version: 3
+    supported repository versions: 3 5
+    upgrade supported from repository versions: 0 1 2 4
+
+Jörn
+"""]]
diff --git a/doc/sync.mdwn b/doc/sync.mdwn
index ade34d48d..37b2b1b45 100644
--- a/doc/sync.mdwn
+++ b/doc/sync.mdwn
@@ -7,7 +7,7 @@ That works fine, if you don't mind having a central repository.
 
 But it can be harder to use git in a fully decentralized fashion, with no
 central repository and still keep repositories in sync with one another.
-You have to remember to pull from each remote, and merge the appopriate
+You have to remember to pull from each remote, and merge the appropriate
 branch after pulling. It's difficult to *push* to a remote, since git does
 not allow pushes into the currently checked out branch.
 
diff --git a/doc/sync/comment_6_012e9d4468d0b88ee3c5dad3911c3606._comment b/doc/sync/comment_6_012e9d4468d0b88ee3c5dad3911c3606._comment
new file mode 100644
index 000000000..24381237f
--- /dev/null
+++ b/doc/sync/comment_6_012e9d4468d0b88ee3c5dad3911c3606._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkI9AR8BqG4RPw_Ov2lnDCJWMuM6WMRobQ"
+ nickname="Dav"
+ subject="Syncing only a specific branch"
+ date="2013-11-24T17:48:22Z"
+ content="""
+By default, `git annex sync` will sync to all remotes, unless you specify a remote. So, I have to specify, e.g., `git annex sync origin`. I can simplify this with aliases, I suppose, but I do a lot of teaching non-programmer scientists... so it'd be nice to be able to configure this (so beginning users don't have to keep track of as many things).
+
+Is there (or will there be) a way to do this?
+"""]]
diff --git a/doc/sync/comment_7_6276e100d1341f1a0be368f54de0ae7b._comment b/doc/sync/comment_7_6276e100d1341f1a0be368f54de0ae7b._comment
new file mode 100644
index 000000000..c40a31200
--- /dev/null
+++ b/doc/sync/comment_7_6276e100d1341f1a0be368f54de0ae7b._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 7"
+ date="2013-11-26T20:08:33Z"
+ content="""
+I feel that syncing with all remotes by default is the right thing for git annex sync to do. 
+"""]]
diff --git a/doc/testimonials/comment_1_2bf439f7a3bc3d6fab91849017946182._comment b/doc/testimonials/comment_1_2bf439f7a3bc3d6fab91849017946182._comment
new file mode 100644
index 000000000..2c5facd1f
--- /dev/null
+++ b/doc/testimonials/comment_1_2bf439f7a3bc3d6fab91849017946182._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="gjost"
+ ip="108.205.152.179"
+ subject="distributed digital repository"
+ date="2013-11-14T00:39:49Z"
+ content="""
+I am in the process of building a distributed digital repository using Git and git-annex as a foundation. Our project is to collect and preserve archival-quality audio and video from multiple bandwidth-challenged remote sites. We're using git-annex to help us sneakernet the metadata and binaries around and to maintain multiple copies in geographically separate locations. Git very neatly addresses the problem of tracking changes, while git-annex makes it possible to track the flow of information through a network of distributed repositories. 
+"""]]
diff --git a/doc/tips/Crude_Windows_Sync.mdwn b/doc/tips/Crude_Windows_Sync.mdwn
new file mode 100644
index 000000000..88138a0b1
--- /dev/null
+++ b/doc/tips/Crude_Windows_Sync.mdwn
@@ -0,0 +1,35 @@
+Here's a workaround to start syncing folders on Windows right now. It's a bit command line heavy, so you might need to set this up for your users. But I would much rather do this than use some other syncing solution and then have to migrate.
+
+(1) Create a remote server git annex repository with the assistant on Linux or Mac.
+
+(2) [Install git](http://git-scm.com/) on the Windows machine.
+
+(3) [Install git-annex for Windows](http://git-annex.branchable.com/install/Windows/) on the Windows machine. Don't forget to run the installer as administrator.
+
+(4) Run _Git Bash_ from the system menu, and run these commands to clone your repository.
+
+    ssh-keygen
+    cat .ssh/id_rsa.pub | ssh username@my-server.com "cat >> ~/.ssh/authorized_keys"
+    git clone username@my-server.com:/path/to/annex
+    cd annex
+    git annex init
+
+(5) Create a script that will trigger a full sync
+
+    echo '
+    #!/bin/bash
+    git annex sync
+    git annex get *
+    git annex add .
+    git annex sync
+    git annex copy * --to origin  
+    ' > sync.sh
+    chmod +x sync.sh
+    ./sync.sh
+
+(6) Copy the "Git Bash" shortcut from your windows menu to your desktop, and change the link target to:
+
+    C:\Program Files\Git\bin\sh.exe" --login -i "annex/sync.sh"
+
+Now ask your users to run this shortcut before and after they change files. You can also put it into the "autostart" folder to sync at boot.
+
diff --git a/doc/tips/Decentralized_repository_behind_a_Firewall.mdwn b/doc/tips/Decentralized_repository_behind_a_Firewall.mdwn
index 6a9eb241b..9e347c73f 100644
--- a/doc/tips/Decentralized_repository_behind_a_Firewall.mdwn
+++ b/doc/tips/Decentralized_repository_behind_a_Firewall.mdwn
@@ -25,7 +25,7 @@ Now you can run normal annex operations, as long as the port forwarding shell is
 
     git annex sync
     git annex get on-the-go some/big/file
-    git annex status
+    git annex info
 
 You can add more computers by repeating with a different port, e.g. 2202 or 2203 (or any other).
 
diff --git a/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone.mdwn b/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone.mdwn
new file mode 100644
index 000000000..1afac15d5
--- /dev/null
+++ b/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone.mdwn
@@ -0,0 +1,32 @@
+I have an annex that syncs my personal files on all my computers. It works great. Phones are different.
+
+For one, everything's a bit slower to sync, there's battery considerations, and I just don't need every last old file on my phone. Then there's some files I explicitly don't want on my phone in case it gets lost, like family pictures, passport scans, or private keys.
+
+But I still want photos, videos and voice recordings I make on my phone to be synced to my server. A transfer repo would work, but I want to keep them. Then there's my PDF book collection; that would certainly be nice to always have around in case I have half on hour on a bus. And my music collection ought to be around as well.
+
+So I came up with this solution, and I'm very happy with it.
+
+    include=Music/* or include=Books/* or present
+
+This will sync my music and book collections to my phone whenever I add something new on my computers, and it will sync and keep anything I add to the annex on my phone. Best of all worlds! Impressed how flexible preferred content is. More full-sync folders can be added like this: 
+
+    include=Music/* or include=Books/* or Notes/* or present
+
+To add them, I first had to figure out the uuid of my phone repo. So I added a new tab on android, and did
+
+    cd /sdcard/annex
+    git config annex.uuid
+
+Then I went to one of my computers, and did
+
+    git annex vicfg
+
+And changed the line
+
+    content [phone-uuid] = standard
+
+to
+
+    content [phone-uuid] = include=Music/* or include=Books/* or Notes/* or present
+
+And waited for it to sync.
diff --git a/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone/comment_1_393d1636bb313530be383a075bd3440a._comment b/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone/comment_1_393d1636bb313530be383a075bd3440a._comment
new file mode 100644
index 000000000..8938684f8
--- /dev/null
+++ b/doc/tips/The_perfect_preferred_content_settings_for_my_android_phone/comment_1_393d1636bb313530be383a075bd3440a._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-16T17:29:03Z"
+ content="""
+That's great, that's how I hoped people would be able to use preferred content settings.
+
+I'd suggest adding support for archive directories to this. So if you create a file on the phone and are done with it, you can move it to an archive directory, and it will then be dropped from the phone once it reaches an archive repository. 
+
+This should accomplish that. (Untested)
+
+`((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and (include=Music/* or include=Books/* or present)`
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt.mdwn b/doc/tips/fully_encrypted_git_repositories_with_gcrypt.mdwn
index c94a8b053..5934747f0 100644
--- a/doc/tips/fully_encrypted_git_repositories_with_gcrypt.mdwn
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt.mdwn
@@ -1,4 +1,4 @@
-[git-remote-gcrypt](https://github.com/blake2-ppc/git-remote-gcrypt/)
+[git-remote-gcrypt](https://github.com/joeyh/git-remote-gcrypt/)
 adds support for encrypted remotes to git. The git-annex 
 [[gcrypt special remote|special_remotes/gcrypt]] allows git-annex to
 also store its files in such repositories. Naturally, git-annex encrypts
@@ -28,12 +28,21 @@ only you can see it.
 First, you need to set up a gpg key. You might consider generating a
 special purpose key just for this use case, since you may end up wanting to
 put the key on multiple machines that you would not trust with your
-main gpg key. You need to tell git-annex the keyid of the key.
+main gpg key.
+
+You need to tell git-annex the keyid of the key when setting up the
+encrypted repository:
 
 	git init --bare /mnt/encryptedbackup
 	git annex initremote encryptedbackup type=gcrypt gitrepo=/mnt/encryptedbackup keyid=$mykey
 	git annex sync encryptedbackup
+
+Now you can copy (or even move) files to the repository. After
+sending files to it, you'll probably want to do a sync, which pushes
+the git repository changes to it as well.
+
 	git annex copy --to encryptedbackup ...
+	git annex sync encryptedbackup
 
 Note that if you lose your gpg key, it will be *impossible* to get the
 data out of your encrypted backup. You need to find a secure way to store a
@@ -66,16 +75,22 @@ First, on the server, run:
 While this will work without git-annex being installed on the server, it
 is recommended to have it installed.)
 
-Now, in your existing git-annex repository:
+Now, in your existing git-annex repository, set up the encrypted remote:
 
 	git annex initremote encryptedrepo type=gcrypt gitrepo=ssh://my.server/home/me/encryptedrepo keyid=$mykey
 	git annex sync encryptedrepo
-	git annex copy --to encryptedrepo ...
 
 If you're going to be sharing this repository with others, be sure to also
 include their keyids, by specifying keyid= repeatedly.
 
-Now that the repo is set up, anyone who has access to it and has one of the keys
+Now you can copy (or even move) files to the repository. After
+sending files to it, you'll probably want to do a sync, which pushes
+the git repository changes to it as well.
+
+	git annex copy --to encryptedrepo ...
+	git annex sync encryptedbackup
+
+Anyone who has access to the repo it and has one of the keys
 used to encrypt it can check it out:
 
 	git clone gcrypt::ssh://my.server/home/me/encryptedrepo myrepo
@@ -91,7 +106,7 @@ Using it this way, git-annex does not store large files on the hosting site; it'
 only used to store your git repository itself.
 
 	git remote add encrypted gcrypt::ssh://hostingsite/myrepo.git
-	git config git push encrypted master git-annex
+	git push encrypted master git-annex
 
 Now you can carry on using git-annex with your new repository. For example,
 `git annex sync` will sync with it.
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_10_4440a80d64c60c7312d5c405d54e607a._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_10_4440a80d64c60c7312d5c405d54e607a._comment
new file mode 100644
index 000000000..4ee70bcd7
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_10_4440a80d64c60c7312d5c405d54e607a._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="tanen"
+ ip="83.128.159.25"
+ subject="comment 10"
+ date="2013-11-04T17:58:36Z"
+ content="""
+> \"We could symetrically encrypt the repository with a keyfile that's stored in the repository itself\"
+> Then you would need to decrypt the repository in order get the key you need to decrypt the repository. The impossibility of this design is why I didn't do that!
+
+Sorry, I ment that the file containing the symmetric encryption key should obviously not be used to encrypt itself, it would be stored in the repository \"unencrypted\" (but protected with a passphrase)
+
+> store a non-encrypted gpg key alongside the repsitory encrypted with it, but then you have to rely on a passphrase for all your security.
+
+Exactly. I think such a mode be a great addition. It might not be as secure as encryption based on a private key - depending on the passphrase strength -, but it would certainly be a lot more convenient and portable (and still much more secure than the shared encryption method).
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_1_5c54690586f2a781905ea4b25aa1147f._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_1_5c54690586f2a781905ea4b25aa1147f._comment
new file mode 100644
index 000000000..71305e650
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_1_5c54690586f2a781905ea4b25aa1147f._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="Is there a way to specify a preferred pgp key?"
+ date="2013-11-01T18:57:38Z"
+ content="""
+Hi,
+
+I think the current behavior of the special remote is a bit annoying when one has several pgp keys. 
+
+Indeed, I've followed the encrypted backup drive example specifying the id of a dedicated key in the initremote step, so far so good. Doing that, I was prompted for my key phrase by the gnome keyring daemon, as expected. 
+
+The annoying part starts right at the git annex sync step. Indeed, when git-remote-gcrypt tries to decrypt the manifest from the encrypted remote, rather than trying only the key specified during the initremote step, it tries all my (secret) keys. This means that I get prompted for the key phrase of all those keys (minus the correct one which is already unlocked...). 
+
+In the future, this might possible to avoid by allowing gcrypt to fetch a preferred key from git config and to use with the --try-secret-key option available gnupg 2.1.x. But for 1.x or 2.0.x, the simpler option --default-key does not seem to alter the order in which keys are tried to decrypt the manifest. Also, it does not seem to be a problem of the gnome keyring daemon, but rather a gpg problem as when the daemon is replaced by the standard gpg-agent, the same problem occurs. 
+
+Meanwhile, is there any way to avoid this problem? 
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_2_07feedb4348f8c31176cc744c19368a1._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_2_07feedb4348f8c31176cc744c19368a1._comment
new file mode 100644
index 000000000..b154263fe
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_2_07feedb4348f8c31176cc744c19368a1._comment
@@ -0,0 +1,21 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="A possible solution"
+ date="2013-11-02T14:22:13Z"
+ content="""
+I'm answering to myself :-). A possible solution to the annoying pass phrase asking with current gnupg is to use a specialized secret keyring. One first exports the secret key used for this repository in a specific keyring as follows:
+
+`gpg --export-secret-keys keyid | gpg --import --no-default-keyring --secret-keyring mygitannexsecret.gpg`
+
+This will create a keyring in $HOME/.gnupg with only the specific key. 
+
+Then, in the git-remote-gcrypt shell script, gpg should be called as follows 
+
+`gpg --no-default-keyring --secret-keyring mygitannexsecret.gpg -q -d ...`
+
+when decrypting the manifest in order to try only the specific key. This behavior can be easily triggered via some git configuration variable.
+
+Any comment?
+
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_3_c2f873dffa015f1d72ad0c3921909316._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_3_c2f873dffa015f1d72ad0c3921909316._comment
new file mode 100644
index 000000000..0ce74d767
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_3_c2f873dffa015f1d72ad0c3921909316._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-02T17:32:28Z"
+ content="""
+Fabrice, I've filed a bug report about this: <https://github.com/blake2-ppc/git-remote-gcrypt/issues/9>
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_4_f8a6e4415f4fe6da14f6a3b7334bc952._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_4_f8a6e4415f4fe6da14f6a3b7334bc952._comment
new file mode 100644
index 000000000..9b1307df4
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_4_f8a6e4415f4fe6da14f6a3b7334bc952._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="tanen"
+ ip="83.128.159.25"
+ subject="comment 4"
+ date="2013-11-03T22:35:07Z"
+ content="""
+The way I would want to setup git-annex (assistant) is \"Wuala/Spideroak style\": two computers with a full checkout of the repository, changes automatically being synced between them, even if the two computers are never online simultaneously, and encryption should be done locally: the (special) remote should not be able to view file listings or content. 
+
+Do I understand it correctly that the gcrypt remote is the only way to make this happen? I tried to create such a setup via the webapp but failed. Adding the repository and remote (via \"Encrypt with GnuPG key\") on the first computer went OK*, but trying to enable that remote on the other computer fails: clicking enable asks me for the SSH password, but after that I just get redirected to a blank screen, with nothing to see in the logfile after the succesful call to ssh-keygen. No entry for the second computer is being added to authorized_keys on the remote.
+
+Perhaps this is because at this point the assistant is unable to actually parse the content of the encrypted repository? I tried importing the private key that was used while creating the repository on the other computer, but that made no difference.
+
+Thinking about this for a while, I believe gpg keys aren't actually particularly suited for this usecase. Even without the bug above, one would either have to awkwardly copy a private key to all hosts that are syncing to the repository; or, every time a new (or reinstalled) host wants to sync the repository, you would manually have to add the new keyid to the config and do the forced push + GCRYPT_FULL_REPACK, presumably having to reupload your entire history. Apart from this, having to backup a private key (outside of your git-annex based backups!) would be quite inconvenient.
+
+How would you feel about adding a new mode of operation where encryption is simply based on a passphrase? We could symetrically encrypt the repository with a keyfile that's stored in the repository itself, protecting the keyfile with a passphrase which - if stored at all - would be stored on the individual computers, outside of the repository.
+
+*although it erroneously used \"E0D2F776E7F674E3\" as key-id while the actual id is E7F674E3; where did that other half come from?
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_5_11b8e82d2a234f65b58b823e71c6d6a2._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_5_11b8e82d2a234f65b58b823e71c6d6a2._comment
new file mode 100644
index 000000000..8e767254c
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_5_11b8e82d2a234f65b58b823e71c6d6a2._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 5"
+ date="2013-11-04T04:40:53Z"
+ content="""
+> How would you feel about adding a new mode of operation where encryption is simply based on a passphrase? We could symetrically encrypt the repository with a keyfile that's stored in the repository itself, protecting the keyfile with a passphrase which - if stored at all - would be stored on the individual computers, outside of the repository.
+
+Isn't that what the regular shared-encryption remote already does?  Except it doesn't put a passphrase on the key, because anyone who has access to the local repo wouldn't need access to the remote one anyway.
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_6_3e41948e1beffcf279bb05ef8e61cc07._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_6_3e41948e1beffcf279bb05ef8e61cc07._comment
new file mode 100644
index 000000000..1a5d7f6e1
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_6_3e41948e1beffcf279bb05ef8e61cc07._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="comment 6"
+ date="2013-11-04T07:39:21Z"
+ content="""
+> _How would you feel about adding a new mode of operation where encryption is simply based on a passphrase? We could symetrically encrypt the repository with a keyfile that's stored in the repository itself, protecting the keyfile with a passphrase which - if stored at all - would be stored on the individual computers, outside of the repository._
+
+As Adam wrote, without a passphrase, this is the shared encryption method. With an encrypted key, this is more or less the hybrid (default) scheme. The thing is that you have to share a secret to have a encrypted remote. I don't use the webapp, so I don't know what's happening in your case, but this is how it should work with the command line tools. First Alice create the encrypted remote with her pgp key. As far as I understand, git annex creates (via gpg) a  key for a symmetric cypher which is stored in the repository, encrypted with Alice public key. If Alice wants to share the repository with Bob, she must either give a key pair (so the private key also, of course) to Bob or ask Bob for his public key. In the first case, Bob can clone the repository directly (upon reception of the key pair), while in the second case, Alice has to active Bob's public key (with `git annex enableremote myremote keyid+=bobsId`). In this case, again as far as I understand, the symmetric key is reencrypted for both Alice and Bob in the repo. 
+
+I understand that you tried the first case with the webapp and that it did not work. I had a similar problem documented in this [http://git-annex.branchable.com/bugs/git-annex-shell:_gcryptsetup_permission_denied](bug). Maybe you could had some comments to this bug description? 
+
+> _*although it erroneously used \"E0D2F776E7F674E3\" as key-id while the actual id is E7F674E3; where did that other half come from?_
+
+This is the long id of your pgp key (16 characters as opposed to 8 for the short id).
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_7_4ce0b26b25b336f07b2e27246cdfba3e._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_7_4ce0b26b25b336f07b2e27246cdfba3e._comment
new file mode 100644
index 000000000..dfb2a3b92
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_7_4ce0b26b25b336f07b2e27246cdfba3e._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="tanen"
+ ip="83.128.159.25"
+ subject="comment 7"
+ date="2013-11-04T09:01:13Z"
+ content="""
+Thanks for the responses. Please correct me if I'm wrong, but the way I understood it, using the shared encryption scheme creates a conflict between \"changes being synced between them, even if the two computers are never online simultaneously\" and \"encryption should be done locally: the (special) remote should not be able to view file listings or content.\"
+
+- If I use shared encryption \"the webapp way\", only the file contents will be rsynced to the remote, not the repository itself. This means that different hosts are unable to sync unless they are online simultaneously, so that commit data can be sent directly between them via XMPP. In practice, this would mean my hosts are never synced (because I don't keep my home computer running when I leave for work, and vice versa)
+
+- If I use shared encryption and additionally put the repository itself on a remote, that remote would have the keys to fully decrypt the repository, that's not acceptable.
+
+Reading through the docs again, the hybrid scheme actually seems to be closer to what I want than the shared scheme, but it still has a major downside: the encryption only applies to the files itself, so in order to get \"offline sync\" there still has to be a 'remote' for the repository itself, which will contain all your metadata unencrypted. And also it would depend on the user being able to manually setup and backup a set of gpg keys instead of just memorizing a secure passphrase.
+
+@Fabrice Looks like the bug you found could very well be the cause of the problem I had; I'll try it again when a new version is available.
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_8_49aa34d75d24a2066baa8a585bc9c2e9._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_8_49aa34d75d24a2066baa8a585bc9c2e9._comment
new file mode 100644
index 000000000..86f3f5cad
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_8_49aa34d75d24a2066baa8a585bc9c2e9._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkbpbjP5j8MqWt_K4NASwv0WvB8T4rQ-pM"
+ nickname="Fabrice"
+ subject="comment 8"
+ date="2013-11-04T10:31:56Z"
+ content="""
+I think you are (at least partially) right. Of course, the only way to sync completely computers that are not on together is to use either a usb drive or a third always on computer. (I've to confess I did not understand first when I read git annex docs, shame on me ;-) If you don't want to trust completely this computer (I don't, for instance), you must :
+
+* use an encrypted git repository on this computer;
+
+* and use either hybrid or pubkey encryption. 
+
+But contrarily to what you seem to imply (I hope I understand you correctly), if you do that, the third computer can still figure out a few things (usage patterns, such as where connections come from), but that's all. You've got full sync and everything is encrypted, both the git part and the files handled by the annex. This applied only to encrypted git special remotes as other remotes do not store the git part.
+"""]]
diff --git a/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_9_3784e0c828cd60b6a9075c2d32d070cc._comment b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_9_3784e0c828cd60b6a9075c2d32d070cc._comment
new file mode 100644
index 000000000..24e5f5b83
--- /dev/null
+++ b/doc/tips/fully_encrypted_git_repositories_with_gcrypt/comment_9_3784e0c828cd60b6a9075c2d32d070cc._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 9"
+ date="2013-11-04T17:07:55Z"
+ content="""
+\"We could symetrically encrypt the repository with a keyfile that's stored in the repository itself\"
+
+Then you would need to decrypt the repository in order get the key you need to decrypt the repository. The impossibility of this design is why I didn't do that!
+
+It would certainly be possible to store a non-encrypted gpg key alongside the repsitory encrypted with it, but then you have to rely on a passphrase for all your security.
+
+You should file a bug report for the bug you saw..
+"""]]
diff --git a/doc/tips/migrating_two_seperate_disconnected_directories_to_git_annex.mdwn b/doc/tips/migrating_two_seperate_disconnected_directories_to_git_annex.mdwn
index 7bddd64b9..1209d1217 100644
--- a/doc/tips/migrating_two_seperate_disconnected_directories_to_git_annex.mdwn
+++ b/doc/tips/migrating_two_seperate_disconnected_directories_to_git_annex.mdwn
@@ -31,7 +31,7 @@ On `angela`, we want to synchronise the git annex metadata with `marcos`. We nee
     git init
     git remote add marcos marcos.example.com:/srv/mp3
     git fetch marcos
-    git annex status # this should display the two repos
+    git annex info # this should display the two repos
     git annex add .
 
 This will, again, checksum all files and add them to git annex. Once that is done, you can verify that the files are really the same as marcos with `whereis`:
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository.mdwn b/doc/tips/recovering_from_a_corrupt_git_repository.mdwn
new file mode 100644
index 000000000..084f76852
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository.mdwn
@@ -0,0 +1,17 @@
+I have found this the most reliable way to recover from a corrupt git repository. I have had a lot of them lately, there might be a regression in btrfs in Ubuntu's Linux 3.8.0-33 (!).
+
+1. Create a clone of a known good repository.
+2. Add the clone as an object alternate to the broken repository.
+3. Do a `git-repack -a -d` to lift the external objects into repo-local packs.
+4. Remove the clone
+
+[[!format sh """
+$ cd /tmp/
+$ git clone good-host:/path/to/good-repo
+$ cd /home/user/broken-repo
+$ echo /tmp/good-repo/.git/objects/ > .git/objects/info/alternates
+$ git repack -a -d
+$ rm -rf /tmp/good-repo
+"""]]
+
+... and push early, push often. ;-)
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_1_f5827be97f78dbae113a5ba0c9ced896._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_1_f5827be97f78dbae113a5ba0c9ced896._comment
new file mode 100644
index 000000000..d212e23f3
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_1_f5827be97f78dbae113a5ba0c9ced896._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-11T16:01:59Z"
+ content="""
+Better, since version 4.20131024, `git annex repair` can be run to automatically do this, and more. (Including recovering data in corrupt git repositories that you forgot to push!)
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_2_e98df7275bb032308bb87e3607bdde32._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_2_e98df7275bb032308bb87e3607bdde32._comment
new file mode 100644
index 000000000..c018c4ca5
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_2_e98df7275bb032308bb87e3607bdde32._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 2"
+ date="2013-11-12T16:14:50Z"
+ content="""
+I am using git-annex 20131106 and I tried `git annex repair` first. It seems git is making assumptions that if I have object A then I must have object B that A depends on. Or maybe it freaks out because the object is not missing, just full of zeroes. I haven't done any analysis on exactly what situation causes this. When I have time, I will.
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_3_11bece6dfac090edbcd783b266c482a3._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_3_11bece6dfac090edbcd783b266c482a3._comment
new file mode 100644
index 000000000..63f443a31
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_3_11bece6dfac090edbcd783b266c482a3._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 3"
+ date="2013-11-12T16:17:42Z"
+ content="""
+Luckily, so far the objects getting corrupted have been in past commits (maybe only in packfiles?), not the latest ones, so I have been able to recover even though HEAD has been unique to the local repo.
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_4_86e99017f7585ac2f76753051214637e._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_4_86e99017f7585ac2f76753051214637e._comment
new file mode 100644
index 000000000..8d454fc3e
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_4_86e99017f7585ac2f76753051214637e._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 4"
+ date="2013-11-12T17:10:06Z"
+ content="""
+Hm. This is bad. My hunch that btrfs was the culprit seems to have been wrong. After having switched things around, along with lots of `git annex sync` in various places, I now have a corrupt repo on ext4. It must be git or git-annex that does something wrong.
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_c8953732ce353cdf0c4fb81ddc98c04a._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_c8953732ce353cdf0c4fb81ddc98c04a._comment
new file mode 100644
index 000000000..eeb3ceef2
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_c8953732ce353cdf0c4fb81ddc98c04a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 6"
+ date="2013-11-12T18:10:21Z"
+ content="""
+If you can reliably corrupt a git repository, it's highly likely your hardware (disk or memory) is broken.
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_d0da84df0241dc6ccf0aa0c7598917df._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_d0da84df0241dc6ccf0aa0c7598917df._comment
new file mode 100644
index 000000000..16b2329b9
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_6_d0da84df0241dc6ccf0aa0c7598917df._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 6"
+ date="2013-11-12T17:22:01Z"
+ content="""
+This is my symptom too: [[forum/Git annex 'corrupting' itself]]
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_7_addf49556e4c33d55a41c393f519d0a4._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_7_addf49556e4c33d55a41c393f519d0a4._comment
new file mode 100644
index 000000000..5047bcca4
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_7_addf49556e4c33d55a41c393f519d0a4._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 7"
+ date="2013-11-12T18:12:49Z"
+ content="""
+> I tried git annex repair first. It seems git is making assumptions that if I have object A then I must have object B that A depends on. Or maybe it freaks out because the object is not missing
+
+`git annex repair` is supposed to deal with these situations. If it fails to fix such a broken repository, please file a detailed bug report, ideally with a link to a copy of the repository.
+"""]]
diff --git a/doc/tips/recovering_from_a_corrupt_git_repository/comment_8_505a2fc2b841fe8eb419801f923ef35f._comment b/doc/tips/recovering_from_a_corrupt_git_repository/comment_8_505a2fc2b841fe8eb419801f923ef35f._comment
new file mode 100644
index 000000000..78144b893
--- /dev/null
+++ b/doc/tips/recovering_from_a_corrupt_git_repository/comment_8_505a2fc2b841fe8eb419801f923ef35f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://id.clacke.se/"
+ nickname="clacke"
+ subject="comment 8"
+ date="2013-11-14T10:00:20Z"
+ content="""
+Several machines started showing this behavior around 4.20131106 or 4.20131101. I will find a way to reproduce when I can find the time.
+"""]]
diff --git a/doc/tips/using_gitolite_with_git-annex/comment_16_8e5039e6655fc80dc863b6cdf44ef02a._comment b/doc/tips/using_gitolite_with_git-annex/comment_16_8e5039e6655fc80dc863b6cdf44ef02a._comment
new file mode 100644
index 000000000..5e0e6acd6
--- /dev/null
+++ b/doc/tips/using_gitolite_with_git-annex/comment_16_8e5039e6655fc80dc863b6cdf44ef02a._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmbo-yMzW_lkBrS4ICNn5XMr8saYtI1_WY"
+ nickname="Douglas"
+ subject="Any further info regarding gitolite support?"
+ date="2013-11-14T03:20:31Z"
+ content="""
+We have reached the same point as the previous poster from 25 days ago. 
+$ git annex copy --to origin
+FATAL: suspicious characters loitering about 'git-annex-shell 'configlist' '/~/testing''
+
+  Remote origin does not have git-annex installed; setting remote.origin.annex-ignore
+git-annex: cannot determine uuid for origin
+
+Anyone actually have this working?
+"""]]
diff --git a/doc/tips/using_gitolite_with_git-annex/comment_17_9c40e1da8bb44f7207e802377f5cf923._comment b/doc/tips/using_gitolite_with_git-annex/comment_17_9c40e1da8bb44f7207e802377f5cf923._comment
new file mode 100644
index 000000000..57152bad7
--- /dev/null
+++ b/doc/tips/using_gitolite_with_git-annex/comment_17_9c40e1da8bb44f7207e802377f5cf923._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawm9tgeFE5v-arAYYftSv3yUTI5Q4qB2C9M"
+ nickname="Khaije"
+ subject="comment 17"
+ date="2013-11-23T02:14:12Z"
+ content="""
+my gitolite.rc is available at https://gist.github.com/khaije1/7609848
+
+For whatever reason I've found this to be very simple to get working so I'd guess there's a missing ingredient somewhere. The combination of gitolite and git-annex is valuable to me so I'll add documents to the url above in hopes it will assist some people with getting the same value.
+
+"""]]
diff --git a/doc/tips/yet_another_simple_disk_usage_like_utility/comment_1_41b212bde8bc88d2a5dea93bd0dc75f1._comment b/doc/tips/yet_another_simple_disk_usage_like_utility/comment_1_41b212bde8bc88d2a5dea93bd0dc75f1._comment
index 3a88e855e..4c3e3c22b 100644
--- a/doc/tips/yet_another_simple_disk_usage_like_utility/comment_1_41b212bde8bc88d2a5dea93bd0dc75f1._comment
+++ b/doc/tips/yet_another_simple_disk_usage_like_utility/comment_1_41b212bde8bc88d2a5dea93bd0dc75f1._comment
@@ -4,6 +4,6 @@
  subject="comment 1"
  date="2013-07-12T19:36:28Z"
  content="""
-Ah, I just found that git annex status can do the same :)
+Ah, I just found that git annex info can do the same :)
 Disregard this.
 """]]
diff --git a/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp.mdwn b/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp.mdwn
new file mode 100644
index 000000000..e102606ca
--- /dev/null
+++ b/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp.mdwn
@@ -0,0 +1,5 @@
+Especially on Mac OSX (and Windows, and maybe Android), it would be great to be able to check in the webapp if an upgrade is available. A deeper integration with these OS would be even better: for example on Mac OSX, an icon on the status bar list available upgrades for some programs, including LibreOffice and others which are not installed by default.
+
+Also, it would be great to be able to download and install git-annex upgrades directly from the webapp.
+
+> comprehensively [[done]]; [[design/assistant/upgrading]] --[[Joey]]
diff --git a/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp/comment_1_c904182f6bff8b1a42070bbc038eb34e._comment b/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp/comment_1_c904182f6bff8b1a42070bbc038eb34e._comment
new file mode 100644
index 000000000..750e3b83a
--- /dev/null
+++ b/doc/todo/Check_if_an_upgrade_is_available_in_the_webapp/comment_1_c904182f6bff8b1a42070bbc038eb34e._comment
@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.246"
+ subject="comment 1"
+ date="2013-11-15T20:51:18Z"
+ content="""
+I have thought about doing this, especially if there is ever a security hole in git-annex.
+
+All it needs is a file containing the version number to be written along-side the git-annex build, and git-annex knowing if it was built as a standalone build, and should check that.
+
+As for actually performing the upgrade:
+
+* Easy on Linux
+* Not sure on OSX.. Is it possible to use hdiutil attach to replace a dmg while a program contained in it is currently running?
+* Probably impossible on Android, at least not without using double the space. Probably better to get git-annex into an app store.
+* Doable on Windows, but would need git-annex to be distributed in a form that was not a installer.exe.
+"""]]
diff --git a/doc/todo/Not_working_on_Android-x86.mdwn b/doc/todo/Not_working_on_Android-x86.mdwn
new file mode 100644
index 000000000..56f2ce962
--- /dev/null
+++ b/doc/todo/Not_working_on_Android-x86.mdwn
@@ -0,0 +1,19 @@
+[[!meta title="Android is only autobuilt for arm, not x86 or mips"]]
+
+### Please describe the problem.
+
+git-annex doesn't start on [Android-x86](http://www.android-x86.org) in VirtualBox (version 4.1.18-dfsg-2+deb7u1).
+
+On Android 4.2.2 (android-x86-4.2-20130228.iso) it starts the terminal which prints nothing but `[Terminal session finished]`.
+On Android 4.3 (android-x86-4.3-20130725.iso) it starts the terminal and prints:
+
+    In mgmain JNI_OnLoad
+    
+    [Terminal session finished]
+
+The browser/webapp is never started.
+
+### What version of git-annex are you using? On what operating system?
+
+Version 1.0.52 for Android. I made sure to install the correct APK files for each version of Android.
+
diff --git a/doc/todo/Not_working_on_Android-x86/comment_1_5eec4d7530c9df68f1bd1b1ca7021ef5._comment b/doc/todo/Not_working_on_Android-x86/comment_1_5eec4d7530c9df68f1bd1b1ca7021ef5._comment
new file mode 100644
index 000000000..4bcca0ab4
--- /dev/null
+++ b/doc/todo/Not_working_on_Android-x86/comment_1_5eec4d7530c9df68f1bd1b1ca7021ef5._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-22T16:37:36Z"
+ content="""
+git-annex is a native binary, and is currently only being built for arm android.
+
+Is Android on x86 a thing used on real-world hardware? I have only seen it in the context of a developer's test environment.
+
+The instructions for building git-annex from source for Android should work on x86. The ghc-android build would need to be tweaked to build a cross compiler targeting that architecture. This can be done by editing settings near the top of ghc-android's `build.sh`.
+
+I am going to move this from bugs/ to todo/ after posting this comment, because it is certiantly not a bug, but a wishlist item at best.
+"""]]
diff --git a/doc/todo/Option_for_browser_to_launch_webapp_with.mdwn b/doc/todo/Option_for_browser_to_launch_webapp_with.mdwn
new file mode 100644
index 000000000..dae601169
--- /dev/null
+++ b/doc/todo/Option_for_browser_to_launch_webapp_with.mdwn
@@ -0,0 +1,7 @@
+Firefox is my default browser, but as we all know, it doesn't load quickly.  If I don't have Firefox running but I want to access the git-annex webapp, I'd rather launch the webapp in some small, quick browser like QupZilla than wait for Firefox to load.
+
+Could git-annex have a setting, maybe a "webapp --browser" option and/or a setting in the config file, to specify the browser to launch?
+
+> git-annex uses the standard `git config web.browser` if you set it.
+> [[done]]
+> --[[Joey]]
diff --git a/doc/todo/Show_repo_type_in_repo_list.mdwn b/doc/todo/Show_repo_type_in_repo_list.mdwn
new file mode 100644
index 000000000..40fbe6537
--- /dev/null
+++ b/doc/todo/Show_repo_type_in_repo_list.mdwn
@@ -0,0 +1 @@
+It would be helpful to show each repo's type in the list.
diff --git a/doc/todo/Show_repo_type_in_repo_list/comment_1_ac6eb1072ef902a094b79dd8e0917c4d._comment b/doc/todo/Show_repo_type_in_repo_list/comment_1_ac6eb1072ef902a094b79dd8e0917c4d._comment
new file mode 100644
index 000000000..10c0c17df
--- /dev/null
+++ b/doc/todo/Show_repo_type_in_repo_list/comment_1_ac6eb1072ef902a094b79dd8e0917c4d._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-02T23:45:39Z"
+ content="""
+Currently if you go to the edit page for the repository, it shows some information about it, including its type and often its location, at the bottom of the page.
+
+I tend to feel that putting anything else in the repo list would result in it being too cluttered.
+"""]]
diff --git a/doc/todo/Show_repo_type_in_repo_list/comment_2_6979c487f707a724a048d20e2e5744e6._comment b/doc/todo/Show_repo_type_in_repo_list/comment_2_6979c487f707a724a048d20e2e5744e6._comment
new file mode 100644
index 000000000..7d4a36324
--- /dev/null
+++ b/doc/todo/Show_repo_type_in_repo_list/comment_2_6979c487f707a724a048d20e2e5744e6._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmNu4V5fvpLlBhaCUfXXOB0MI5NXwh8SkU"
+ nickname="Adam"
+ subject="comment 2"
+ date="2013-11-02T23:59:16Z"
+ content="""
+I understand.  Well, here's what I'm looking at right now.  :)
+
+[[http://alphapapa.net/outbox/view.png]]
+
+I just think it would be very useful to say \"Client\" or \"Transfer\" or \"Full Backup\" next to each one, and there's often plenty of room, depending on the size of the window.  Especially when one's trying to wrap one's head around git-annex, being reminded what each repo is for would help a lot.  Otherwise you basically have to put it in the name or description yourself...so why not just go ahead and show it?  :)
+
+Another option might be to have an icon for each type.
+"""]]
diff --git a/doc/todo/Show_repo_type_in_repo_list/comment_3_529254a6cc20de7259d60a3cbc5ccaf7._comment b/doc/todo/Show_repo_type_in_repo_list/comment_3_529254a6cc20de7259d60a3cbc5ccaf7._comment
new file mode 100644
index 000000000..3f8b82695
--- /dev/null
+++ b/doc/todo/Show_repo_type_in_repo_list/comment_3_529254a6cc20de7259d60a3cbc5ccaf7._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 3"
+ date="2013-11-03T00:19:34Z"
+ content="""
+I'd be happy to put in some icons if someone finds some good (and suitably licensed) ones that cover the different types of repositories.
+"""]]
diff --git a/doc/todo/Sync_repo_names__63__.mdwn b/doc/todo/Sync_repo_names__63__.mdwn
new file mode 100644
index 000000000..d3bb59f04
--- /dev/null
+++ b/doc/todo/Sync_repo_names__63__.mdwn
@@ -0,0 +1,10 @@
+It's very confusing to me that the same repo viewed from different client systems can have different names and descriptions.  This implies that making changes to a remote repo from one system only affects how that system sees the repo, but it seems to affect how the entire git-annex "pair" or "network of repos" sees it.
+
+I think it would be good if the names and descriptions of repos were synced across clients.
+
+> The descriptions of repositories are synced. (They're stored in git-annex:uuid.log)
+> 
+> git allows for the same repository to be referred to using as many different remote names as you want to set up. git-annex inherits this,
+> and I can't see this changing; there are very good reasons for remotes to
+> have this flexability. [[done]]
+> --[[Joey]] 
diff --git a/doc/todo/checksum_verification_on_transfer.mdwn b/doc/todo/checksum_verification_on_transfer.mdwn
index e87907d56..c9d505aec 100644
--- a/doc/todo/checksum_verification_on_transfer.mdwn
+++ b/doc/todo/checksum_verification_on_transfer.mdwn
@@ -1,6 +1,6 @@
 Since most file transfers, particularly to/from encrypted special remotes involve git-annex streaming through the contents of the file anyway, it should be possible to add a verification of the checksum nearly for free. The main thing needed is probably a faster haskell checksum library than Data.Digest.Pure.Sha, which is probably slow enough to be annoying.
 
-I have not verified if an upload could be aborted before sending the data to the remote if a checksum failure is detected. It may be dependent on the individual special remote implementations. Some probably stream the encrypted data directly out the wire, while others need to set up a temp file to run a command on. It would certianly be possible to at least make the upload abort and fail if a bad checksum was detected.
+I have not verified if an upload could be aborted before sending the data to the remote if a checksum failure is detected. It may be dependent on the individual special remote implementations. Some probably stream the encrypted data directly out the wire, while others need to set up a temp file to run a command on. It would certainly be possible to at least make the upload abort and fail if a bad checksum was detected.
 
 Doing the same for downloads is less useful, because the data is there locally to be fscked. The real advantage would be doing the check for uploads, to ensure that hard-to-detect corrupted files don't reach special remotes.
 
diff --git a/doc/todo/direct_mode_guard.mdwn b/doc/todo/direct_mode_guard.mdwn
index 7322cec63..bb7f90897 100644
--- a/doc/todo/direct_mode_guard.mdwn
+++ b/doc/todo/direct_mode_guard.mdwn
@@ -20,3 +20,86 @@ add`. The git wrapper could instead be another program, or it could be
 something like `git annex git add`
 
 --[[Joey]]
+
+----
+
+Or, no git wrapper could be provided. Limit the commands to only git-annex
+commands. This should be all that is needed to manage a direct mode
+repository simply, and if the user is doing something complicated that
+needs git access, they can set `GIT_DIR=.git-annex` and be careful not to
+shoot off their foot. (Or can just switch to indirect mode!)
+
+This wins on simplicity, and if it's the wrong choice a git wrapper
+can be added later. --[[Joey]]
+
+---
+
+Implementation: Pretty simple really. Already did the hard lifting to
+support `GIT_DIR`, so only need to override the default git directory
+in direct mode when that's not set to `.git-annex`.
+
+A few things hardcode ".git", including Assistant.Threads.Watcher.ignored
+and `Seek.withPathContents`, and parts of `Git.Construct`.
+
+---
+
+Transition: git-annex should detect when it's in a direct mode repository
+with a .git directory and no .git-annex directory, and transparently
+do the move to transition to the new scheme. (And remember that `git annex
+indirect` needs to move it back.)
+
+# alternative approach: move index
+
+Rather than moving .git, maybe move .git/index?
+
+This would cause git to think that all files in the tree were deleted.
+So git commit -a would make a commit that removes them from git history.
+But, the files in the work tree are not touched by this.
+
+Also, git checkout, git merge, and other things that manipulate the work
+tree refuse to do anything if they'd change a file that they think is
+untracked.
+
+Hmm, this does't solve the user accidentially running git add on an annexed
+file; the whole file still gets added.
+
+# alternative approach: fake bare repo
+
+Set core.bare to true.  This prevents all work tree operations, 
+so prevents any foot shooting. It still lets the user run commands like
+git log, even on files in the tree, and git fetch, and push, and git
+config, etc.
+
+Even better, it integrates with other tools, like `mr`, so they know
+it's a git repo.
+
+This seems really promising. But of course, git-annex has its own set of
+behaviors in a bare repo, so will need to recognise that this repo is not
+really bare, and avoid them.
+
+> [[done]]!!  --[[Joey]]
+
+(Git may also have some bare repo behaviors that are unwanted. One example
+is that git allows pushes to the current branch in a bare repo, 
+even when `receive.denyCurrentBranch` is set.)
+
+> This is indeed a problem. Indeed, `git annex sync` successfully
+> pushes changes to the master branch of a fake bare direct mode repo.
+> 
+> And then, syncing in the repo that was pushed to causes the changes
+> that were pushed to the master branch to get reverted! This happens
+> because sync commits; commit sees that files are staged in index
+> differing from the (pushed) master, and commits the "changes"
+> which revert it.
+> 
+> Could fix this using an update hook, to reject the updated of the master
+> branch. However, won't work on crippled filesystems! (No +x bit)
+> 
+> Could make git annex sync detect this. It could reset the master
+> branch to the last one committed, before committing. Seems very racy
+> and hard to get right!
+>
+> Could make direct mode operate on a different branch, like
+> `annex/direct/master` rather than `master`. Avoid pushing to that
+> branch (`git annex sync` can map back from it to `master` and push there
+> instead). A bit clumsy, but works.
diff --git a/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__.mdwn b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__.mdwn
new file mode 100644
index 000000000..8ce910ac3
--- /dev/null
+++ b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__.mdwn
@@ -0,0 +1,5 @@
+I've an external USB hard disc attached to my (fritzbox) router that is only accessible through SMB/CIFS. I'd like have all my annexed files on this drive in kind of direct-mode so that I can also access the files without git-annex.
+
+I tried to put a direct-mode repo on the drive but this is painfully slow. The git-annex process than runs on my desktop and accesses the repo over SMB over the slow fritzbox over USB.
+
+I'd wish that git-annex could be told to just use a (mounted) folder as a direct-mode remote.
diff --git a/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_1_5ed9a2336b432b842c1805add6d96509._comment b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_1_5ed9a2336b432b842c1805add6d96509._comment
new file mode 100644
index 000000000..bff1b2fcd
--- /dev/null
+++ b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_1_5ed9a2336b432b842c1805add6d96509._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-23T19:03:58Z"
+ content="""
+It's not clear to me what you are requesting here.
+
+You seem to say that running git-annex inside a mountpoint is slow. Ok. So, what possible changes to git-annex could make it fast, given that the bottleneck is the SMB/USB?
+"""]]
diff --git a/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_2_e6ba58c5c31ba23a4575f1189689946f._comment b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_2_e6ba58c5c31ba23a4575f1189689946f._comment
new file mode 100644
index 000000000..d60cb2d4d
--- /dev/null
+++ b/doc/todo/dumb_plaindir_remote___40__e.g._for_NAS_mounts__41__/comment_2_e6ba58c5c31ba23a4575f1189689946f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnR6E5iUghMWdUGlbA9CCs8DKaoigMjJXw"
+ nickname="Efraim"
+ subject="comment 2"
+ date="2013-11-26T09:26:53Z"
+ content="""
+perhaps he's looking to be able to expand the addurl option to include file://path/to/video.mp4, or for over smb://... , to import a file without changing its location to being inside the annex.
+"""]]
diff --git a/doc/todo/quvi_0.9_support.mdwn b/doc/todo/quvi_0.9_support.mdwn
new file mode 100644
index 000000000..36280452a
--- /dev/null
+++ b/doc/todo/quvi_0.9_support.mdwn
@@ -0,0 +1,8 @@
+quvi 0.9 has a completely different interface; git-annex needs to be made
+to detect and use it.
+
+I have already fixed the worst problem, which caused git-annex addurl to
+think that every url was a valid quvi url. --[[Joey]]
+
+> [[done]], 0.9 is supported, although the version is detected at build
+> time. --[[Joey]]
diff --git a/doc/todo/smudge/comment_3_4e7c25fe24a1e71f58a8354fa64f41c2._comment b/doc/todo/smudge/comment_3_4e7c25fe24a1e71f58a8354fa64f41c2._comment
new file mode 100644
index 000000000..cd64b7001
--- /dev/null
+++ b/doc/todo/smudge/comment_3_4e7c25fe24a1e71f58a8354fa64f41c2._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawn1QhtPvsRBV7pfaDW_ZTPFv_ZIxSzQ8Rg"
+ nickname="Paul Léo"
+ subject="comment 3"
+ date="2013-11-13T20:41:52Z"
+ content="""
+> SHA1 has a harder job. Would not want to re-sha1 the file every time, probably. So it'd need a local cache of file stat info, mapped to known objects.
+
+I think that is not true? If gits wants the file to be cleaned, it thinks that the file was changed. So you would have to SHA1 it anyway if you don't want rely on WORM (which git already does in the first step anyway).
+"""]]
diff --git a/doc/todo/special_remote_for_amazon_glacier.mdwn b/doc/todo/special_remote_for_amazon_glacier.mdwn
index 0fa77b527..9b8b9d74e 100644
--- a/doc/todo/special_remote_for_amazon_glacier.mdwn
+++ b/doc/todo/special_remote_for_amazon_glacier.mdwn
@@ -3,7 +3,7 @@ long-term archival.
 
 The main difficulty is that glacier is organized into vaults, and accessing
 a file in a vault takes ~4 hours. A naive implementation would make `git
-annex get` wait for 4 hours, which is certianly not reasonable.
+annex get` wait for 4 hours, which is certainly not reasonable.
 
 One approach I am pondering is to make each glacier vault a separate
 special remote. You could then request git-annex to spin up a remote, and
diff --git a/doc/todo/windows_support.mdwn b/doc/todo/windows_support.mdwn
index 08327dba8..a8cbd6db8 100644
--- a/doc/todo/windows_support.mdwn
+++ b/doc/todo/windows_support.mdwn
@@ -9,7 +9,15 @@ now! --[[Joey]]
 * rsync special remotes are known buggy.
 * Bad file locking, it's probably not safe to run more than one git-annex
   process at the same time on Windows.
-* No support for the assistant or webapp.
 * Ssh connection caching does not work on Windows, so `git annex get`
   has to connect twice to the remote system over ssh per file, which
   is much slower than on systems supporting connection caching.
+* Webapp doesn't build yet.
+* `git annex watch` builds, but does not quite work.
+* `git annex assistant` builds, but has not been tested, and is known
+  to not download any files. (transferrer doesn't built yet)
+* watch and assistant cannot be built with cabal. Possibly due to too many
+  files overflowing command line length limit at link stage.
+  To build a binary with them: 
+  `ghc --make git-annex.hs -threaded -XPackageImports -DWITH_ASSISTANT=1 -DWITH_WIN32NOTIFY=1`
+  (should add all the other flags cabal uses)
diff --git a/doc/todo/wishlist:_an___34__assistant__34___for_web-browsing_--_tracking_the_sources_of_the_downloads/comment_7_15bf62e46db4b84ed3156f550f03de42._comment b/doc/todo/wishlist:_an___34__assistant__34___for_web-browsing_--_tracking_the_sources_of_the_downloads/comment_7_15bf62e46db4b84ed3156f550f03de42._comment
index 6c4d579c1..484db1e81 100644
--- a/doc/todo/wishlist:_an___34__assistant__34___for_web-browsing_--_tracking_the_sources_of_the_downloads/comment_7_15bf62e46db4b84ed3156f550f03de42._comment
+++ b/doc/todo/wishlist:_an___34__assistant__34___for_web-browsing_--_tracking_the_sources_of_the_downloads/comment_7_15bf62e46db4b84ed3156f550f03de42._comment
@@ -6,7 +6,7 @@
  content="""
 A less round-about method would be to have the webapp listen for links dropped into its page. You could then have the webapp open in a tab, and just drag urls there to add them to the annex.
 
-I'm not sure if it's possible to intercept drags into a tab. Default browser behavior is certianly to redirect the tab to the url dropped into it.
+I'm not sure if it's possible to intercept drags into a tab. Default browser behavior is certainly to redirect the tab to the url dropped into it.
 
 If someone finds out how to do this, I will build it.
 """]]
diff --git a/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync.mdwn b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync.mdwn
new file mode 100644
index 000000000..873988eea
--- /dev/null
+++ b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync.mdwn
@@ -0,0 +1 @@
+The `annex.largefiles` feature is very nice to mix annexed files with normal git managed files. I'd like to be able to configure this setting on the webapp and that the configuration directive would be synchronized accross all remotes.
diff --git a/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_1_db632de391ce9fce42af51a770ed3aeb._comment b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_1_db632de391ce9fce42af51a770ed3aeb._comment
new file mode 100644
index 000000000..e402d26c3
--- /dev/null
+++ b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_1_db632de391ce9fce42af51a770ed3aeb._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.47"
+ subject="comment 1"
+ date="2013-11-05T16:46:28Z"
+ content="""
+It might make sense to sync this across remotes and have it edited with `git annex vicfg`
+
+Putting it in the webapp would need some nice interface for constructing the underlying expression. Might be doable for at least simple filtering (ie, files larger than XX or with extensions .A, .B, .C). I tend to think of this as a setting for people comfortable with the command line though.
+"""]]
diff --git a/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_2_4a0931d9884054d764fde315d4fe4851._comment b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_2_4a0931d9884054d764fde315d4fe4851._comment
new file mode 100644
index 000000000..0e24014d2
--- /dev/null
+++ b/doc/todo/wishlist:_annex.largefiles_configuration_in_webapp_and_sync/comment_2_4a0931d9884054d764fde315d4fe4851._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawne_amN4fko4p5cRY_9EYwaYuJKNn7LRio"
+ nickname="Tobias"
+ subject="feedback"
+ date="2013-11-05T21:23:11Z"
+ content="""
+> It might make sense to sync this across remotes and have it edited with git annex vicfg
+
+That would be great!
+
+> Putting it in the webapp would need some nice interface for constructing the underlying expression. Might be doable for at least simple filtering (ie, files larger than XX or with extensions .A, .B, .C). I tend to think of this as a setting for people comfortable with the command line though.
+
+I could live with a simple filtering interface without too many fancy stuff. The fancy stuff could be done on the command line if needed...
+"""]]
diff --git a/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration.mdwn b/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration.mdwn
new file mode 100644
index 000000000..f0d27d0b1
--- /dev/null
+++ b/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration.mdwn
@@ -0,0 +1 @@
+When starting the assistant when logging in to the system (`--autostart`) it choses a new port an secret everytime. Having the assistant open in a pinned firefox tab which automatically restores when firefox starts we need to get the url from `.git/annex/url` and copy/paste it into the pinned tab. It would be very nice to have a configuration option which assigns a fixed port and secret so everytime the assistant is autostarted it uses the same settings and firefox is happy to open it automatically on start.
diff --git a/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration/comment_1_be53b8456eed7eadad5d4b8465c8a42b._comment b/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration/comment_1_be53b8456eed7eadad5d4b8465c8a42b._comment
new file mode 100644
index 000000000..651937802
--- /dev/null
+++ b/doc/todo/wishlist:_assistant_autostart_port_and_secret_configuration/comment_1_be53b8456eed7eadad5d4b8465c8a42b._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.64"
+ subject="comment 1"
+ date="2013-11-22T16:58:51Z"
+ content="""
+It's impossible to guarantee a program will be able to get a particular port. Any other program could be using that port number.
+
+This is why `git annex webapp` opens the webapp using whatever url the assistant has picked. I recommend that rather than using a pinned tab, you make an icon on your desktop that runs `git annex webapp`, and use that to open the app when you want it, much as you'd open any other app. If you wanted to, you could make your system run `git annex webapp` on startup instead of `git annex assistant --autostart`, and you'd get the browser tab opened automatically on start.
+"""]]
diff --git a/doc/todo/wishlist:_detection_of_merge_conflicts.mdwn b/doc/todo/wishlist:_detection_of_merge_conflicts.mdwn
new file mode 100644
index 000000000..1b4caeff0
--- /dev/null
+++ b/doc/todo/wishlist:_detection_of_merge_conflicts.mdwn
@@ -0,0 +1,13 @@
+A conflict during sync or merge is something that requires user intervention, or at least notification. For that reason it would be nice if git annex returned a nonzero exit status when such a conflict happened during a sync or a merge. This is what git does after a conflicting pull, and would make it easier to spot a conflict in automated syncs without having to parse annex output or the logs.
+
+> Good idea, [[done]]. --[[Joey]] 
+
+Also, it would be nice if your new `git annex status` were able to inform about remaining conflicts in the repo, for instance by reporting files with variant-XXX suffix.
+
+> Hmm, that would need a separate pass through the whole tree, since
+> currently it can use `git ls-files` to find only modified/deleted/new
+> files. I would rather not make the new `git annex status` slower for
+> this.
+> 
+> It would be possible to add it to `git annex info` (old `status`)
+> which already has to look through the entire work tree.
diff --git a/doc/todo/wishlist:_disable_automatic_commits.mdwn b/doc/todo/wishlist:_disable_automatic_commits.mdwn
index 5b39c60c7..14c131796 100644
--- a/doc/todo/wishlist:_disable_automatic_commits.mdwn
+++ b/doc/todo/wishlist:_disable_automatic_commits.mdwn
@@ -33,4 +33,4 @@ detecting manual commits wouldn't be a stretch.
 > You can do this now by pausing committing via the webapp,
 > or setting `annex.autocommit=false`.
 > 
-> The assustant probably doesn't push such commits yet.
+> The assistant probably doesn't push such commits yet.
diff --git a/doc/todo/wishlist:_encrypted_git_remote_on_hosting_site_from_webapp.mdwn b/doc/todo/wishlist:_encrypted_git_remote_on_hosting_site_from_webapp.mdwn
new file mode 100644
index 000000000..b7b1bad0c
--- /dev/null
+++ b/doc/todo/wishlist:_encrypted_git_remote_on_hosting_site_from_webapp.mdwn
@@ -0,0 +1 @@
+It would be great to be able to do **private encrypted git remote on hosting site** and **multiuser encrypted git remote on hosting site** as explained in [[tips/fully encrypted git repositories with gcrypt]] through the webapp. I think it's a pretty common usecase that can be very useful for people not owning a proper server.
diff --git a/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__.mdwn b/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__.mdwn
new file mode 100644
index 000000000..420fb882c
--- /dev/null
+++ b/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__.mdwn
@@ -0,0 +1,10 @@
+I recently tried to use unannex for a large repo and it failed because the repo size was more than half the disk size.  Unannex should work incrementally so this isn't a problem.
+
+Proposed solution:
+copy a file, hash it, iff hash check is okay, delete from objects, continue to next file
+
+> That won't work, because multiple files can point to a key.
+> 
+> I am not happy with unannex's behavior, but I was less happy
+> when people were constantly filing bugs about it misbehaving in that
+> situttion. If you dislike the copying, use --fast. [[done]] --[[Joey]]
diff --git a/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__/comment_1_067b29fc47d26b9da0766f9810684ae8._comment b/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__/comment_1_067b29fc47d26b9da0766f9810684ae8._comment
new file mode 100644
index 000000000..372bb621f
--- /dev/null
+++ b/doc/todo/wishlist:_incremental_unannex___40__currently_requires_twice_the_size_of_repo_to_complete__41__/comment_1_067b29fc47d26b9da0766f9810684ae8._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="GLITTAH"
+ ip="78.108.63.46"
+ subject="comment 1"
+ date="2013-11-19T18:15:15Z"
+ content="""
+Perhaps when unannex is invoked, it could check to see if there is enough disk space before it begins copying files.  Maybe even warn the user of too little disk space and remind them of --fast.
+
+(Sorry for the dupe!)
+"""]]
diff --git a/doc/todo/wishlist:_make_git_annex_reinject_work_in_direct_mode.mdwn b/doc/todo/wishlist:_make_git_annex_reinject_work_in_direct_mode.mdwn
index 41c8e574b..ffdee8840 100644
--- a/doc/todo/wishlist:_make_git_annex_reinject_work_in_direct_mode.mdwn
+++ b/doc/todo/wishlist:_make_git_annex_reinject_work_in_direct_mode.mdwn
@@ -16,3 +16,6 @@ Description:	Ubuntu 12.04.2 LTS
 Release:	12.04
 Codename:	precise
 ~~~~
+
+> [[fixed|done]]. Why did I take so long to do this, it was a trivial 1
+> word change! --[[Joey]]
diff --git a/doc/todo/wishlist:_simpler_gpg_usage/comment_2_6fc874b6c391df242bd2592c4a65eae8._comment b/doc/todo/wishlist:_simpler_gpg_usage/comment_2_6fc874b6c391df242bd2592c4a65eae8._comment
index 29eb11622..2e12d86d4 100644
--- a/doc/todo/wishlist:_simpler_gpg_usage/comment_2_6fc874b6c391df242bd2592c4a65eae8._comment
+++ b/doc/todo/wishlist:_simpler_gpg_usage/comment_2_6fc874b6c391df242bd2592c4a65eae8._comment
@@ -4,7 +4,7 @@
  subject="comment 2"
  date="2012-04-29T02:39:20Z"
  content="""
-The encryption uses a symmetric cipher that is stored in the git repository already. It's just stored encrypted to the various gpg keys that have been configured to use it. It would certianly be possible to store the symmetric cipher unencrypted in the git repo. 
+The encryption uses a symmetric cipher that is stored in the git repository already. It's just stored encrypted to the various gpg keys that have been configured to use it. It would certainly be possible to store the symmetric cipher unencrypted in the git repo. 
 
 I don't see your idea of gpg-options saving any work. It would still require you to do key distribution and run commands in each repo to set it up.
 """]]
diff --git a/doc/todo/wishlist:_swift_backend/comment_4_4d97d12ddd99834788e94648c8eebef9._comment b/doc/todo/wishlist:_swift_backend/comment_4_4d97d12ddd99834788e94648c8eebef9._comment
new file mode 100644
index 000000000..21fa52aaf
--- /dev/null
+++ b/doc/todo/wishlist:_swift_backend/comment_4_4d97d12ddd99834788e94648c8eebef9._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawm5Z8wzidsumLYQnHdrVxpCx8vsd9llSlg"
+ nickname="Emanuele"
+ subject="comment 4"
+ date="2013-11-22T15:52:42Z"
+ content="""
+OVH is offering free accounts with 25GB of storage on their hubiC service: https://hubic.com/en/
+
+The API documentation (based on OAuth2 and OpenStack Swift) is available at https://api.hubic.com/
+"""]]
diff --git a/doc/todo/wishlist_degraded_files.mdwn b/doc/todo/wishlist_degraded_files.mdwn
new file mode 100644
index 000000000..0b265c5eb
--- /dev/null
+++ b/doc/todo/wishlist_degraded_files.mdwn
@@ -0,0 +1,5 @@
+This is an idea to have a small placeholder file that is put into
+place when the file's actual content is not available in the local
+annex.
+
+Details being discussed here: <http://bugs.debian.org/728552>
diff --git a/doc/upgrades.mdwn b/doc/upgrades.mdwn
index 6cf54477c..5cf4093dc 100644
--- a/doc/upgrades.mdwn
+++ b/doc/upgrades.mdwn
@@ -18,10 +18,18 @@ conflicts first before upgrading git-annex.
 
 ## Upgrade events, so far
 
+### v4 -> v5 (git-annex version 5.x)
+
+v5 is only used for [[direct_mode]]. The upgrade from v4 to v5 is handled
+automatically.
+
+This upgrade involves changing direct mode repositories to operate with
+core.bare=true.
+
 ### v3 -> v4 (git-annex version 4.x)
 
-v4 is only used for [[direct_mode]], and no upgrade needs to be done from
-existing v3 repositories, they will continue to work.
+v4 was only used for [[direct_mode]], to ensure that a version of git-annex
+that understands direct mode was used with a direct mode repository. 
 
 ### v2 -> v3 (git-annex version 3.x)
 
diff --git a/doc/users/clacke.mdwn b/doc/users/clacke.mdwn
new file mode 100644
index 000000000..c48cd311f
--- /dev/null
+++ b/doc/users/clacke.mdwn
@@ -0,0 +1,3 @@
+Claes Wallin (韋嘉誠)
+
+[[https://microca.st/clacke]]
diff --git a/git-annex.cabal b/git-annex.cabal
index 2498bf106..da78c7def 100644
--- a/git-annex.cabal
+++ b/git-annex.cabal
@@ -1,5 +1,5 @@
 Name: git-annex
-Version: 4.20131101
+Version: 5.20131120
 Cabal-Version: >= 1.8
 License: GPL-3
 Maintainer: Joey Hess <joey@kitenet.net>
@@ -56,7 +56,11 @@ Flag Production
   Description: Enable production build (slower build; faster binary)
 
 Flag Android
-  Description: Building for Android
+  Description: Cross building for Android
+  Default: False
+
+Flag AndroidSplice
+  Description: Building to get TH splices for Android
   Default: False
 
 Flag TestSuite
@@ -74,6 +78,10 @@ Flag Quvi
 Flag CryptoHash
   Description: Enable use of cryptohash for checksumming
 
+Flag EKG
+  Description: Enable use of EKG to monitor git-annex as it runs (at http://localhost:4242/)
+  Default: False
+
 Executable git-annex
   Main-Is: git-annex.hs
   Build-Depends: MissingH, hslogger, directory, filepath,
@@ -101,7 +109,7 @@ Executable git-annex
     Build-Depends: unix
 
   if flag(TestSuite)
-    Build-Depends: HUnit
+    Build-Depends: tasty, tasty-hunit, tasty-quickcheck
     CPP-Options: -DWITH_TESTSUITE
 
   if flag(TDFA)
@@ -120,14 +128,10 @@ Executable git-annex
     Build-Depends: DAV (>= 0.3), http-conduit, xml-conduit, http-types
     CPP-Options: -DWITH_WEBDAV
 
-  if flag(Assistant) && ! os(windows) && ! os(solaris)
+  if flag(Assistant) && ! os(solaris)
     Build-Depends: stm (>= 2.3)
     CPP-Options: -DWITH_ASSISTANT
 
-  if flag(Android)
-    Build-Depends: data-endian
-    CPP-Options: -D__ANDROID__
-
   if flag(Assistant)
     if os(linux) && flag(Inotify)
       Build-Depends: hinotify
@@ -137,17 +141,27 @@ Executable git-annex
         Build-Depends: hfsevents
         CPP-Options: -DWITH_FSEVENTS
       else
-        if (! os(windows) && ! os(solaris) && ! os(linux))
-          if flag(Android)
-            Build-Depends: hinotify
-            CPP-Options: -DWITH_INOTIFY
-          else
-            CPP-Options: -DWITH_KQUEUE
-            C-Sources: Utility/libkqueue.c
+        if os(windows)
+          Build-Depends: Win32-notify
+          CPP-Options: -DWITH_WIN32NOTIFY
+        else
+          if (! os(solaris) && ! os(linux))
+            if flag(Android)
+              Build-Depends: hinotify
+              CPP-Options: -DWITH_INOTIFY
+            else
+              CPP-Options: -DWITH_KQUEUE
+              C-Sources: Utility/libkqueue.c
 
   if os(linux) && flag(Dbus)
     Build-Depends: dbus (>= 0.10.3)
     CPP-Options: -DWITH_DBUS
+  
+  if flag(Android)
+    Build-Depends: data-endian
+    CPP-Options: -D__ANDROID__ -DANDROID_SPLICES
+  if flag(AndroidSplice)
+    CPP-Options: -DANDROID_SPLICES
 
   if flag(Webapp) && (! os(windows))
     Build-Depends:
@@ -177,6 +191,11 @@ Executable git-annex
     Build-Depends: aeson
     CPP-Options: -DWITH_QUVI
 
+  if flag(EKG)
+    Build-Depends: ekg
+    GHC-Options: -with-rtsopts=-T
+    CPP-Options: -DWITH_EKG
+
 source-repository head
   type: git
   location: git://git-annex.branchable.com/
diff --git a/git-recover-repository.hs b/git-recover-repository.hs
deleted file mode 100644
index 3e348f5bb..000000000
--- a/git-recover-repository.hs
+++ /dev/null
@@ -1,42 +0,0 @@
-{- git-recover-repository program
- -
- - Copyright 2013 Joey Hess <joey@kitenet.net>
- -
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-import System.Environment
-import qualified Data.Set as S
-import Data.Tuple.Utils
-
-import Common
-import qualified Git
-import qualified Git.CurrentRepo
-import qualified Git.Fsck
-import qualified Git.Repair
-import qualified Git.Config
-import qualified Git.Branch
-
-header :: String
-header = "Usage: git-recover-repository"
-
-usage :: a
-usage = error $ "bad parameters\n\n" ++ header
-
-parseArgs :: IO Bool
-parseArgs = do
-	args <- getArgs
-	return $ or $ map parse args
-  where
-	parse "--force" = True
-	parse _ = usage
-
-main :: IO ()
-main = do
-	forced <- parseArgs
-	
-	g <- Git.Config.read =<< Git.CurrentRepo.get
-	ifM (fst3 <$> Git.Repair.runRepair forced g)
-		( exitSuccess
-		, exitFailure
-		)
diff --git a/standalone/android/.gitignore b/standalone/android/.gitignore
deleted file mode 100644
index e8792ba9f..000000000
--- a/standalone/android/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-build-utils
-start
diff --git a/standalone/android/Makefile b/standalone/android/Makefile
index 1a2ef0f1a..f5cd67b26 100644
--- a/standalone/android/Makefile
+++ b/standalone/android/Makefile
@@ -2,7 +2,7 @@
 # and builds the Android app.
 
 # Add Android cross-compiler to PATH (as installed by ghc-android)
-ANDROID_CROSS_COMPILER?=$(HOME)/.ghc/android-14/arm-linux-androideabi-4.7/bin
+ANDROID_CROSS_COMPILER?=$(HOME)/.ghc/$(shell cat abiversion)/bin
 PATH:=$(ANDROID_CROSS_COMPILER):$(PATH)
 
 # Paths to the Android SDK and NDK.
@@ -15,6 +15,8 @@ GIT_ANNEX_ANDROID_SOURCETREE?=$(HOME)/.android/git-annex-sourcetree
 
 GITTREE=$(GIT_ANNEX_ANDROID_SOURCETREE)/git/installed-tree
 
+VER=$(shell perl -e '$$_=<>;print m/\((.*?)\)/'<../../CHANGELOG)
+
 build: start
 	if [ ! -e "$(GIT_ANNEX_ANDROID_SOURCETREE)" ]; then $(MAKE) source; fi
 	$(MAKE) $(GIT_ANNEX_ANDROID_SOURCETREE)/openssl/build-stamp
@@ -25,13 +27,14 @@ build: start
 	$(MAKE) $(GIT_ANNEX_ANDROID_SOURCETREE)/git/build-stamp
 	$(MAKE) $(GIT_ANNEX_ANDROID_SOURCETREE)/term/build-stamp
 
+	perl -i -pe 's/(android:versionName=)"[^"]+"/$$1"'$(VER)'"/' $(GIT_ANNEX_ANDROID_SOURCETREE)/term/AndroidManifest.xml
+	
 	# Debug build because it does not need signing keys.
 	cd $(GIT_ANNEX_ANDROID_SOURCETREE)/term && tools/build-debug
 
 	# Install executables as pseudo-libraries so they will be
 	# unpacked from the .apk.
 	mkdir -p $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi
-	cp ../../tmp/androidtree/dist/build/git-annex/git-annex $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.git-annex.so
 	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/busybox/busybox $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.busybox.so
 	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/openssh/ssh $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.ssh.so
 	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/openssh/ssh-keygen $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.ssh-keygen.so
@@ -74,9 +77,17 @@ build: start
 
 	git rev-parse HEAD > $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.version.so
 
+	mkdir -p ../../tmp/4.0 ../../tmp/4.3
+	
+	cp ../../tmp/androidtree/dist/build/git-annex/4.3/git-annex $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.git-annex.so
+	arm-linux-androideabi-strip --strip-unneeded --remove-section=.comment --remove-section=.note $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.git-annex.so
+	cd $(GIT_ANNEX_ANDROID_SOURCETREE)/term && ant debug
+	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/term/bin/Term-debug.apk ../../tmp/4.3/git-annex.apk
+
+	cp ../../tmp/androidtree/dist/build/git-annex/4.0/git-annex $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.git-annex.so
+	arm-linux-androideabi-strip --strip-unneeded --remove-section=.comment --remove-section=.note $(GIT_ANNEX_ANDROID_SOURCETREE)/term/libs/armeabi/lib.git-annex.so
 	cd $(GIT_ANNEX_ANDROID_SOURCETREE)/term && ant debug
-	mkdir -p ../../tmp
-	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/term/bin/Term-debug.apk ../../tmp/git-annex.apk
+	cp $(GIT_ANNEX_ANDROID_SOURCETREE)/term/bin/Term-debug.apk ../../tmp/4.0/git-annex.apk
 
 $(GIT_ANNEX_ANDROID_SOURCETREE)/openssl/build-stamp:
 	cd $(GIT_ANNEX_ANDROID_SOURCETREE)/openssl && CC=$$(which cc) ./Configure android
diff --git a/standalone/android/abiversion b/standalone/android/abiversion
new file mode 100644
index 000000000..4cc4c14cd
--- /dev/null
+++ b/standalone/android/abiversion
@@ -0,0 +1 @@
+android-14/arm-linux-androideabi-4.8
diff --git a/standalone/android/buildchroot b/standalone/android/buildchroot
index b759ae6ce..44337eb0c 100755
--- a/standalone/android/buildchroot
+++ b/standalone/android/buildchroot
@@ -8,6 +8,7 @@ fi
 debootstrap --arch=i386 stable debian-stable-android
 cp $0-inchroot debian-stable-android/tmp
 cp $0-inchroot-asuser debian-stable-android/tmp
+cp $(dirname $0)/abiversion debian-stable-android/tmp
 
 # Don't use these vars in the chroot.
 unset TMP
diff --git a/standalone/android/buildchroot-inchroot-asuser b/standalone/android/buildchroot-inchroot-asuser
index 2cd77b6b7..710e76e46 100755
--- a/standalone/android/buildchroot-inchroot-asuser
+++ b/standalone/android/buildchroot-inchroot-asuser
@@ -29,8 +29,7 @@ mv adt-bundle-linux-x86-* adt-bundle-linux-x86
 rm -rf adt-bundle-linux-x86/eclipse
 
 # The git-annex android Makefile needs this cc symlink.
-ln -s arm-linux-androideabi-gcc \
-	$HOME/.ghc/android-14/arm-linux-androideabi-4.7/bin/cc
+ln -s arm-linux-androideabi-gcc $HOME/.ghc/$(cat /tmp/abiversion)/bin/cc
 
 cd
 git clone git://git-annex.branchable.com/ git-annex
diff --git a/standalone/android/clean-haskell-packages b/standalone/android/clean-haskell-packages
index bffdf00bb..b8c6132d6 100755
--- a/standalone/android/clean-haskell-packages
+++ b/standalone/android/clean-haskell-packages
@@ -2,5 +2,5 @@
 # Removes all currently installed cross-compiled haskell packages
 # except those part of ghc.
 # Useful if the build failed.
-rm -f $(grep -l $HOME/.ghc/android-14/arm-linux-androideabi-4.7/.cabal/lib/ $HOME/.ghc/android-14/arm-linux-androideabi-4.7/lib/*-ghc-*/package.conf.d/*.conf)
-$HOME/.ghc/android-14/arm-linux-androideabi-4.7/arm-linux-androideabi/bin/ghc-pkg recache
+rm -f $(grep -l $HOME/.ghc/$(cat abiversion)/.cabal/lib/ $HOME/.ghc/android-14/arm-linux-androideabi-4.8/lib/*-ghc-*/package.conf.d/*.conf)
+$HOME/.ghc/$(cat abiversion)/arm-linux-androideabi/bin/ghc-pkg recache
diff --git a/standalone/android/haskell-patches/crypto-numbers_build-fix.patch b/standalone/android/haskell-patches/crypto-numbers_build-fix.patch
new file mode 100644
index 000000000..f8bdd1c39
--- /dev/null
+++ b/standalone/android/haskell-patches/crypto-numbers_build-fix.patch
@@ -0,0 +1,235 @@
+From f6ed5c3093111ffe0276f5b5bb6241783611ab1c Mon Sep 17 00:00:00 2001
+From: androidbuilder <androidbuilder@example.com>
+Date: Mon, 11 Nov 2013 01:54:25 +0000
+Subject: [PATCH] hack to build
+
+---
+ Crypto/Number/Basic.hs         |   17 -----------------
+ Crypto/Number/ModArithmetic.hs |   29 -----------------------------
+ Crypto/Number/Prime.hs         |   18 ------------------
+ crypto-numbers.cabal           |    2 +-
+ 4 files changed, 1 insertion(+), 65 deletions(-)
+
+diff --git a/Crypto/Number/Basic.hs b/Crypto/Number/Basic.hs
+index af03052..5de8518 100644
+--- a/Crypto/Number/Basic.hs
++++ b/Crypto/Number/Basic.hs
+@@ -1,8 +1,5 @@
+ {-# LANGUAGE BangPatterns #-}
+ {-# LANGUAGE CPP #-}
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-{-# LANGUAGE UnboxedTuples #-}
+-#endif
+ -- |
+ -- Module      : Crypto.Number.Basic
+ -- License     : BSD-style
+@@ -17,11 +14,7 @@ module Crypto.Number.Basic
+     , areEven
+     ) where
+ 
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-import GHC.Integer.GMP.Internals
+-#else
+ import Data.Bits
+-#endif
+ 
+ -- | sqrti returns two integer (l,b) so that l <= sqrt i <= b
+ -- the implementation is quite naive, use an approximation for the first number
+@@ -60,25 +53,16 @@ sqrti i
+ -- gcde 'a' 'b' find (x,y,gcd(a,b)) where ax + by = d
+ --
+ gcde :: Integer -> Integer -> (Integer, Integer, Integer)
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-gcde a b = (s, t, g)
+-  where (# g, s #) = gcdExtInteger a b
+-        t = (g - s * a) `div` b
+-#else
+ gcde a b = if d < 0 then (-x,-y,-d) else (x,y,d) where
+     (d, x, y)                     = f (a,1,0) (b,0,1)
+     f t              (0, _, _)    = t
+     f (a', sa, ta) t@(b', sb, tb) =
+         let (q, r) = a' `divMod` b' in
+         f t (r, sa - (q * sb), ta - (q * tb))
+-#endif
+ 
+ -- | get the extended GCD of two integer using the extended binary algorithm (HAC 14.61)
+ -- get (x,y,d) where d = gcd(a,b) and x,y satisfying ax + by = d
+ gcde_binary :: Integer -> Integer -> (Integer, Integer, Integer)
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-gcde_binary = gcde
+-#else
+ gcde_binary a' b'
+     | b' == 0   = (1,0,a')
+     | a' >= b'  = compute a' b'
+@@ -102,7 +86,6 @@ gcde_binary a' b'
+              in if u2 >= v2
+                 then loop g x y (u2 - v2) v2 (a2 - c2) (b2 - d2) c2 d2
+                 else loop g x y u2 (v2 - u2) a2 b2 (c2 - a2) (d2 - b2)
+-#endif
+ 
+ -- | check if a list of integer are all even
+ areEven :: [Integer] -> Bool
+diff --git a/Crypto/Number/ModArithmetic.hs b/Crypto/Number/ModArithmetic.hs
+index 031f477..38b22b7 100644
+--- a/Crypto/Number/ModArithmetic.hs
++++ b/Crypto/Number/ModArithmetic.hs
+@@ -26,12 +26,8 @@ module Crypto.Number.ModArithmetic
+ import Control.Exception (throw, Exception)
+ import Data.Typeable
+ 
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-import GHC.Integer.GMP.Internals
+-#else
+ import Crypto.Number.Basic (gcde_binary)
+ import Data.Bits
+-#endif
+ 
+ -- | Raised when two numbers are supposed to be coprimes but are not.
+ data CoprimesAssertionError = CoprimesAssertionError
+@@ -52,13 +48,7 @@ expSafe :: Integer -- ^ base
+         -> Integer -- ^ exponant
+         -> Integer -- ^ modulo
+         -> Integer -- ^ result
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-expSafe b e m
+-    | odd m     = powModSecInteger b e m
+-    | otherwise = powModInteger b e m
+-#else
+ expSafe = exponentiation
+-#endif
+ 
+ -- | Compute the modular exponentiation of base^exponant using
+ -- the fastest algorithm without any consideration for
+@@ -71,11 +61,7 @@ expFast :: Integer -- ^ base
+         -> Integer -- ^ modulo
+         -> Integer -- ^ result
+ expFast =
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-    powModInteger
+-#else
+     exponentiation
+-#endif
+ 
+ -- note on exponentiation: 0^0 is treated as 1 for mimicking the standard library;
+ -- the mathematic debate is still open on whether or not this is true, but pratically
+@@ -84,22 +70,15 @@ expFast =
+ -- | exponentiation_rtl_binary computes modular exponentiation as b^e mod m
+ -- using the right-to-left binary exponentiation algorithm (HAC 14.79)
+ exponentiation_rtl_binary :: Integer -> Integer -> Integer -> Integer
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-exponentiation_rtl_binary = expSafe
+-#else
+ exponentiation_rtl_binary 0 0 m = 1 `mod` m
+ exponentiation_rtl_binary b e m = loop e b 1
+     where sq x          = (x * x) `mod` m
+           loop !0 _  !a = a `mod` m
+           loop !i !s !a = loop (i `shiftR` 1) (sq s) (if odd i then a * s else a)
+-#endif
+ 
+ -- | exponentiation computes modular exponentiation as b^e mod m
+ -- using repetitive squaring.
+ exponentiation :: Integer -> Integer -> Integer -> Integer
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-exponentiation = expSafe
+-#else
+ exponentiation b e m
+     | b == 1    = b
+     | e == 0    = 1
+@@ -107,7 +86,6 @@ exponentiation b e m
+     | even e    = let p = (exponentiation b (e `div` 2) m) `mod` m
+                    in (p^(2::Integer)) `mod` m
+     | otherwise = (b * exponentiation b (e-1) m) `mod` m
+-#endif
+ 
+ --{-# DEPRECATED exponantiation_rtl_binary "typo in API name it's called exponentiation_rtl_binary #-}
+ exponantiation_rtl_binary :: Integer -> Integer -> Integer -> Integer
+@@ -119,17 +97,10 @@ exponantiation = exponentiation
+ 
+ -- | inverse computes the modular inverse as in g^(-1) mod m
+ inverse :: Integer -> Integer -> Maybe Integer
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-inverse g m
+-    | r == 0    = Nothing
+-    | otherwise = Just r
+-  where r = recipModInteger g m
+-#else
+ inverse g m
+     | d > 1     = Nothing
+     | otherwise = Just (x `mod` m)
+   where (x,_,d) = gcde_binary g m
+-#endif
+ 
+ -- | Compute the modular inverse of 2 coprime numbers.
+ -- This is equivalent to inverse except that the result
+diff --git a/Crypto/Number/Prime.hs b/Crypto/Number/Prime.hs
+index 2060f4d..61d37c0 100644
+--- a/Crypto/Number/Prime.hs
++++ b/Crypto/Number/Prime.hs
+@@ -1,8 +1,6 @@
+ {-# LANGUAGE CPP #-}
+ {-# LANGUAGE BangPatterns #-}
+-#if MIN_VERSION_integer_gmp(0,5,1)
+ {-# LANGUAGE MagicHash #-}
+-#endif
+ -- |
+ -- Module      : Crypto.Number.Prime
+ -- License     : BSD-style
+@@ -27,12 +25,7 @@ import Crypto.Number.Generate
+ import Crypto.Number.Basic (sqrti, gcde_binary)
+ import Crypto.Number.ModArithmetic (exponantiation)
+ 
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-import GHC.Integer.GMP.Internals
+-import GHC.Base
+-#else
+ import Data.Bits
+-#endif
+ 
+ -- | returns if the number is probably prime.
+ -- first a list of small primes are implicitely tested for divisibility,
+@@ -75,21 +68,11 @@ findPrimeFromWith rng prop !n
+ -- | find a prime from a starting point with no specific property.
+ findPrimeFrom :: CPRG g => g -> Integer -> (Integer, g)
+ findPrimeFrom rng n =
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-    (nextPrimeInteger n, rng)
+-#else
+     findPrimeFromWith rng (\g _ -> (True, g)) n
+-#endif
+ 
+ -- | Miller Rabin algorithm return if the number is probably prime or composite.
+ -- the tries parameter is the number of recursion, that determines the accuracy of the test.
+ primalityTestMillerRabin :: CPRG g => g -> Int -> Integer -> (Bool, g)
+-#if MIN_VERSION_integer_gmp(0,5,1)
+-primalityTestMillerRabin rng (I# tries) !n =
+-    case testPrimeInteger n tries of
+-        0# -> (False, rng)
+-        _  -> (True, rng)
+-#else
+ primalityTestMillerRabin rng tries !n
+     | n <= 3     = error "Miller-Rabin requires tested value to be > 3"
+     | even n     = (False, rng)
+@@ -126,7 +109,6 @@ primalityTestMillerRabin rng tries !n
+                   | x2 == 1   = False
+                   | x2 /= nm1 = loop' ws ((x2*x2) `mod` n) (r+1)
+                   | otherwise = loop ws
+-#endif
+ 
+ {-
+     n < z -> witness to test
+diff --git a/crypto-numbers.cabal b/crypto-numbers.cabal
+index 05c00c1..8da5e2a 100644
+--- a/crypto-numbers.cabal
++++ b/crypto-numbers.cabal
+@@ -15,7 +15,7 @@ Extra-Source-Files:  Tests/*.hs
+ 
+ Flag integer-gmp
+   Description: Are we using integer-gmp?
+-  Default: True
++  Default: False
+ 
+ Library
+   Build-Depends:     base >= 4 && < 5
+-- 
+1.7.10.4
+
diff --git a/standalone/android/haskell-patches/gnutls_0.1.4-0001-statically-link-with-gnutls.patch b/standalone/android/haskell-patches/gnutls_0.1.4-0001-statically-link-with-gnutls.patch
index 6c4ae0c63..24f17cc6f 100644
--- a/standalone/android/haskell-patches/gnutls_0.1.4-0001-statically-link-with-gnutls.patch
+++ b/standalone/android/haskell-patches/gnutls_0.1.4-0001-statically-link-with-gnutls.patch
@@ -1,27 +1,23 @@
-From c46af28d00a67d372bf59490d288c8cb77bae307 Mon Sep 17 00:00:00 2001
+From 67435289745b2f96fc9d1cd8e0263ef0565e4789 Mon Sep 17 00:00:00 2001
 From: Joey Hess <joey@kitenet.net>
-Date: Sun, 21 Apr 2013 17:14:03 -0400
-Subject: [PATCH] statically link with gnutls
+Date: Tue, 26 Nov 2013 19:18:28 +0000
+Subject: [PATCH] hack gnutls to statically link
 
-This requires libgnutls.a (and no .so) be installed in the ugly hardcoded
-lib dir. When built this way, the haskell gnutls library will link the
-library into executables with no further options.
-
-Also includes dependencies of libgnutls (needed since it's a static
-library).
+This uses a hardcoded path to the library, which includes the
+arm-linux-androideabi-4.8 part. Will need to be changed when that changes..
 ---
- gnutls.cabal |    3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
+ gnutls.cabal |    6 ++----
+ 1 file changed, 2 insertions(+), 4 deletions(-)
 
 diff --git a/gnutls.cabal b/gnutls.cabal
-index a20e7ed..d8f4a1f 100644
+index 5bfe687..ff1d08c 100644
 --- a/gnutls.cabal
 +++ b/gnutls.cabal
-@@ -31,10 +31,11 @@ source-repository this
+@@ -31,16 +31,14 @@ source-repository this
  library
    hs-source-dirs: lib
    ghc-options: -Wall -O2
-+  LD-Options: -L /home/joey/.ghc/android-14/arm-linux-androideabi-4.7/arm-linux-androideabi/sysroot/usr/lib/   -lgcrypt -lgpg-error -lz
++  LD-Options: -L /home/androidbuilder/.ghc/android-14/arm-linux-androideabi-4.8/sysroot/usr/lib/ -l:libgnutls.a -l:libnettle.a -l:libhogweed.a -l:libgmp.a
  
    build-depends:
        base >= 4.0 && < 5.0
@@ -30,6 +26,12 @@ index a20e7ed..d8f4a1f 100644
      , transformers >= 0.2
      , monads-tf >= 0.1 && < 0.2
  
+-  extra-libraries: gnutls
+-  pkgconfig-depends: gnutls
+-
+   exposed-modules:
+     Network.Protocol.TLS.GNU
+ 
 -- 
 1.7.10.4
 
diff --git a/standalone/android/haskell-patches/language-javascript_fix-build-with-new-ghc.patch b/standalone/android/haskell-patches/language-javascript_fix-build-with-new-ghc.patch
new file mode 100644
index 000000000..6182cba44
--- /dev/null
+++ b/standalone/android/haskell-patches/language-javascript_fix-build-with-new-ghc.patch
@@ -0,0 +1,25 @@
+From cb5252db1a0d515da69d9167a8b2facd839940b2 Mon Sep 17 00:00:00 2001
+From: androidbuilder <androidbuilder@example.com>
+Date: Mon, 11 Nov 2013 02:29:06 +0000
+Subject: [PATCH] fix build with new ghc
+
+---
+ src/Language/JavaScript/Parser/Lexer.hs |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Language/JavaScript/Parser/Lexer.hs b/src/Language/JavaScript/Parser/Lexer.hs
+index 79fa9c5..fa96e29 100644
+--- a/src/Language/JavaScript/Parser/Lexer.hs
++++ b/src/Language/JavaScript/Parser/Lexer.hs
+@@ -712,7 +712,7 @@ alex_scan_tkn user orig_input len input s last_acc =
+ 		(offset) = (base +# ord_c)
+ 		(check)  = alexIndexInt16OffAddr alex_check offset
+ 		
+-		(new_s) = if (offset >=# 0#) && (check ==# ord_c)
++		(new_s) = if (tagToEnum# (offset >=# 0#)) && (tagToEnum# (check ==# ord_c))
+ 			  then alexIndexInt16OffAddr alex_table offset
+ 			  else alexIndexInt16OffAddr alex_deflt s
+ 	in
+-- 
+1.7.10.4
+
diff --git a/standalone/android/haskell-patches/socks_0.4.2_0001-remove-IPv6-stuff.patch b/standalone/android/haskell-patches/socks_0.4.2_0001-remove-IPv6-stuff.patch
index fc9569573..c9723f3f7 100644
--- a/standalone/android/haskell-patches/socks_0.4.2_0001-remove-IPv6-stuff.patch
+++ b/standalone/android/haskell-patches/socks_0.4.2_0001-remove-IPv6-stuff.patch
@@ -1,7 +1,7 @@
-From 28e6a6599ee91e15aa7b2f9d25433490f192f22e Mon Sep 17 00:00:00 2001
-From: foo <foo@bar>
-Date: Sat, 21 Sep 2013 23:17:29 +0000
-Subject: [PATCH] remove IPv6 stuff
+From e1a2f80f6bec25921ab645a0aaf1c6422a8917ab Mon Sep 17 00:00:00 2001
+From: dummy <dummy@example.com>
+Date: Mon, 11 Nov 2013 01:06:58 +0000
+Subject: [PATCH] fix
 
 ---
  Network/Socks5/Command.hs  |    8 +-------
@@ -12,10 +12,10 @@ Subject: [PATCH] remove IPv6 stuff
  5 files changed, 2 insertions(+), 28 deletions(-)
 
 diff --git a/Network/Socks5/Command.hs b/Network/Socks5/Command.hs
-index 8ce06ec..222d954 100644
+index db95fbd..fdba5ec 100644
 --- a/Network/Socks5/Command.hs
 +++ b/Network/Socks5/Command.hs
-@@ -12,7 +12,6 @@ module Network.Socks5.Command
+@@ -13,7 +13,6 @@ module Network.Socks5.Command
      , Connect(..)
      , Command(..)
      , connectIPV4
@@ -23,7 +23,7 @@ index 8ce06ec..222d954 100644
      , connectDomainName
      -- * lowlevel interface
      , rpc
-@@ -28,7 +27,7 @@ import qualified Data.ByteString as B
+@@ -29,7 +28,7 @@ import qualified Data.ByteString as B
  import qualified Data.ByteString.Char8 as BC
  import Data.Serialize
  
@@ -32,7 +32,7 @@ index 8ce06ec..222d954 100644
  import Network.Socket.ByteString
  
  import Network.Socks5.Types
-@@ -64,11 +63,6 @@ connectIPV4 socket hostaddr port = onReply <$> rpc_ socket (Connect $ SocksAddre
+@@ -65,11 +64,6 @@ connectIPV4 socket hostaddr port = onReply <$> rpc_ socket (Connect $ SocksAddre
      where onReply (SocksAddrIPV4 h, p) = (h, p)
            onReply _                    = error "ipv4 requested, got something different"
  
@@ -114,14 +114,14 @@ index 7fbec25..17c7c83 100644
  data SocksAddress = SocksAddress !SocksHostAddress !PortNumber
      deriving (Show,Eq,Ord)
 diff --git a/Network/Socks5/Wire.hs b/Network/Socks5/Wire.hs
-index 3ab95a8..2881988 100644
+index 10bd262..a30f32e 100644
 --- a/Network/Socks5/Wire.hs
 +++ b/Network/Socks5/Wire.hs
 @@ -46,12 +46,10 @@ data SocksResponse = SocksResponse
  
- getAddr 1 = SocksAddrIPV4 <$> getWord32be
+ getAddr 1 = SocksAddrIPV4 <$> getWord32host
  getAddr 3 = SocksAddrDomainName <$> (getWord8 >>= getByteString . fromIntegral)
--getAddr 4 = SocksAddrIPV6 <$> (liftM4 (,,,) getWord32le getWord32le getWord32le getWord32le)
+-getAddr 4 = SocksAddrIPV6 <$> (liftM4 (,,,) getWord32host getWord32host getWord32host getWord32host)
  getAddr n = error ("cannot get unknown socket address type: " ++ show n)
  
  putAddr (SocksAddrIPV4 h)         = putWord8 1 >> putWord32host h
diff --git a/standalone/android/haskell-patches/uuid_build-without-v1-uuid-which-needs-network-info.patch b/standalone/android/haskell-patches/uuid_build-without-v1-uuid-which-needs-network-info.patch
new file mode 100644
index 000000000..12cb2a922
--- /dev/null
+++ b/standalone/android/haskell-patches/uuid_build-without-v1-uuid-which-needs-network-info.patch
@@ -0,0 +1,79 @@
+From 87283f9b6f992a7f0e36c7b1bafc288bf2bf106a Mon Sep 17 00:00:00 2001
+From: androidbuilder <androidbuilder@example.com>
+Date: Mon, 11 Nov 2013 02:46:27 +0000
+Subject: [PATCH] build without v1 uuid which needs network-ino
+
+---
+ Data/UUID/Util.hs |   11 -----------
+ Data/UUID/V1.hs   |    2 --
+ uuid.cabal        |    2 --
+ 3 files changed, 15 deletions(-)
+
+diff --git a/Data/UUID/Util.hs b/Data/UUID/Util.hs
+index 581391a..399e508 100644
+--- a/Data/UUID/Util.hs
++++ b/Data/UUID/Util.hs
+@@ -3,7 +3,6 @@ module Data.UUID.Util (
+     UnpackedUUID(..)
+   , unpack, pack
+   , version
+-  , extractMac
+   , extractTime
+   , setTime
+   ) where
+@@ -13,7 +12,6 @@ import Data.Word
+ import Data.Word.Util
+ import Data.Bits
+ import Data.UUID.Internal
+-import Network.Info
+ import Data.Int (Int64)
+ 
+ version :: UUID -> Int
+@@ -43,12 +41,3 @@ extractTime uuid =
+ timeAndVersionToTime :: Word16 -> Word16
+ timeAndVersionToTime tv = tv .&. 0x0FFF
+ 
+-extractMac :: UUID -> Maybe MAC
+-extractMac uuid = 
+-  if version uuid == 1
+-  then Just $ 
+-       MAC (node_0 unpacked) (node_1 unpacked) (node_2 unpacked) (node_3 unpacked) (node_4 unpacked) (node_5 unpacked)
+-  else Nothing
+-  where
+-    unpacked = unpack uuid
+-
+diff --git a/Data/UUID/V1.hs b/Data/UUID/V1.hs
+index 067e729..ca4c235 100644
+--- a/Data/UUID/V1.hs
++++ b/Data/UUID/V1.hs
+@@ -37,8 +37,6 @@ import System.IO.Unsafe
+ 
+ import qualified System.Random as R
+ 
+-import Network.Info
+-
+ import Data.UUID.Builder
+ import Data.UUID.Internal
+ 
+diff --git a/uuid.cabal b/uuid.cabal
+index 0a53059..57b1b86 100644
+--- a/uuid.cabal
++++ b/uuid.cabal
+@@ -32,14 +32,12 @@ Library
+                 cryptohash >= 0.7 && < 0.12,
+                 deepseq == 1.3.*,
+                 hashable (>= 1.1.1.0 && < 1.2.0) || (>= 1.2.1 && < 1.3),
+-                network-info == 0.2.*,
+                 random >= 1.0.1 && < 1.1,
+                 time >= 1.1 && < 1.5
+ 
+  Exposed-Modules:
+    Data.UUID
+    Data.UUID.Util
+-   Data.UUID.V1
+    Data.UUID.V3
+    Data.UUID.V4
+    Data.UUID.V5
+-- 
+1.7.10.4
+
diff --git a/standalone/android/haskell-patches/yesod-form_spliced-TH.patch b/standalone/android/haskell-patches/yesod-form_spliced-TH.patch
index d3c0a3570..486d2aaee 100644
--- a/standalone/android/haskell-patches/yesod-form_spliced-TH.patch
+++ b/standalone/android/haskell-patches/yesod-form_spliced-TH.patch
@@ -1,11 +1,8 @@
-From c5b0db193fd6e9fd6be22891ae988babbfac3ff0 Mon Sep 17 00:00:00 2001
+From f645acc0efbfcba7715cd2b6734f0e9df98f7020 Mon Sep 17 00:00:00 2001
 From: dummy <dummy@example.com>
-Date: Sat, 19 Oct 2013 02:14:38 +0000
-Subject: [PATCH] spliced TH
+Date: Mon, 11 Nov 2013 01:26:56 +0000
+Subject: [PATCH] update
 
-Used EvilSplicer. Needed a few syntax fixes, and a lot of added imports.
-
-Removed some things I don't need, rather than re-splicing to handle a new version.
 ---
  Yesod/Form/Fields.hs    |  771 +++++++++++++++++++++++++++++++++++------------
  Yesod/Form/Functions.hs |  237 ++++++++++++---
@@ -13,10 +10,10 @@ Removed some things I don't need, rather than re-splicing to handle a new versio
  Yesod/Form/MassInput.hs |  233 +++++++++++---
  Yesod/Form/Nic.hs       |   61 +++-
  yesod-form.cabal        |    1 +
- 6 files changed, 1123 insertions(+), 305 deletions(-)
+ 6 files changed, 1122 insertions(+), 306 deletions(-)
 
 diff --git a/Yesod/Form/Fields.hs b/Yesod/Form/Fields.hs
-index b8109df..9bde340 100644
+index 0689859..1e9d49b 100644
 --- a/Yesod/Form/Fields.hs
 +++ b/Yesod/Form/Fields.hs
 @@ -1,4 +1,3 @@
@@ -209,16 +206,16 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
    where showVal = either id (pack . renderHtml)
-@@ -168,7 +233,7 @@ $newline never
- -- | A newtype wrapper around a 'Text' that converts newlines to HTML
+@@ -169,8 +234,6 @@ $newline never
  -- br-tags.
  newtype Textarea = Textarea { unTextarea :: Text }
--    deriving (Show, Read, Eq, PersistField, PersistFieldSql, Ord)
-+    deriving (Show, Read, Eq, PersistField, Ord)
+     deriving (Show, Read, Eq, PersistField, Ord)
+-instance PersistFieldSql Textarea where
+-    sqlType _ = SqlString
  instance ToHtml Textarea where
      toHtml =
          unsafeByteString
-@@ -186,10 +251,18 @@ instance ToHtml Textarea where
+@@ -188,10 +251,18 @@ instance ToHtml Textarea where
  textareaField :: Monad m => RenderMessage (HandlerSite m) FormMessage => Field m Textarea
  textareaField = Field
      { fieldParse = parseHelper $ Right . Textarea
@@ -241,7 +238,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -197,10 +270,19 @@ hiddenField :: (Monad m, PathPiece p, RenderMessage (HandlerSite m) FormMessage)
+@@ -199,10 +270,19 @@ hiddenField :: (Monad m, PathPiece p, RenderMessage (HandlerSite m) FormMessage)
              => Field m p
  hiddenField = Field
      { fieldParse = parseHelper $ maybe (Left MsgValueRequired) Right . fromPathPiece
@@ -265,7 +262,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -208,20 +290,55 @@ textField :: Monad m => RenderMessage (HandlerSite m) FormMessage => Field m Tex
+@@ -210,20 +290,55 @@ textField :: Monad m => RenderMessage (HandlerSite m) FormMessage => Field m Tex
  textField = Field
      { fieldParse = parseHelper $ Right
      , fieldView = \theId name attrs val isReq ->
@@ -329,7 +326,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -293,10 +410,24 @@ emailField = Field
+@@ -295,10 +410,24 @@ emailField = Field
              case Email.canonicalizeEmail $ encodeUtf8 s of
                  Just e -> Right $ decodeUtf8With lenientDecode e
                  Nothing -> Left $ MsgInvalidEmail s
@@ -358,7 +355,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -305,20 +436,78 @@ searchField :: Monad m => RenderMessage (HandlerSite m) FormMessage => AutoFocus
+@@ -307,20 +436,78 @@ searchField :: Monad m => RenderMessage (HandlerSite m) FormMessage => AutoFocus
  searchField autoFocus = Field
      { fieldParse = parseHelper Right
      , fieldView = \theId name attrs val isReq -> do
@@ -449,7 +446,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -329,7 +518,30 @@ urlField = Field
+@@ -331,7 +518,30 @@ urlField = Field
              Nothing -> Left $ MsgInvalidUrl s
              Just _ -> Right s
      , fieldView = \theId name attrs val isReq ->
@@ -481,7 +478,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -342,18 +554,56 @@ selectField :: (Eq a, RenderMessage site FormMessage)
+@@ -344,18 +554,56 @@ selectField :: (Eq a, RenderMessage site FormMessage)
              => HandlerT site IO (OptionList a)
              -> Field (HandlerT site IO) a
  selectField = selectFieldHelper
@@ -550,7 +547,7 @@ index b8109df..9bde340 100644
  
  multiSelectFieldList :: (Eq a, RenderMessage site FormMessage, RenderMessage site msg)
                       => [(msg, a)]
-@@ -376,11 +626,48 @@ multiSelectField ioptlist =
+@@ -378,11 +626,48 @@ multiSelectField ioptlist =
      view theId name attrs val isReq = do
          opts <- fmap olOptions $ handlerToWidget ioptlist
          let selOpts = map (id &&& (optselected val)) opts
@@ -604,7 +601,7 @@ index b8109df..9bde340 100644
          where
              optselected (Left _) _ = False
              optselected (Right vals) opt = (optionInternalValue opt) `elem` vals
-@@ -390,67 +677,172 @@ radioFieldList :: (Eq a, RenderMessage site FormMessage, RenderMessage site msg)
+@@ -392,67 +677,172 @@ radioFieldList :: (Eq a, RenderMessage site FormMessage, RenderMessage site msg)
                 -> Field (HandlerT site IO) a
  radioFieldList = radioField . optionsPairs
  
@@ -828,7 +825,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
    where
-@@ -476,10 +868,25 @@ $newline never
+@@ -478,10 +868,25 @@ $newline never
  checkBoxField :: Monad m => RenderMessage (HandlerSite m) FormMessage => Field m Bool
  checkBoxField = Field
      { fieldParse = \e _ -> return $ checkBoxParser e
@@ -858,7 +855,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = UrlEncoded
      }
  
-@@ -523,49 +930,7 @@ optionsPairs opts = do
+@@ -525,49 +930,7 @@ optionsPairs opts = do
  optionsEnum :: (MonadHandler m, Show a, Enum a, Bounded a) => m (OptionList a)
  optionsEnum = optionsPairs $ map (\x -> (pack $ show x, x)) [minBound..maxBound]
  
@@ -909,7 +906,7 @@ index b8109df..9bde340 100644
  
  selectFieldHelper
          :: (Eq a, RenderMessage site FormMessage)
-@@ -609,9 +974,21 @@ fileField = Field
+@@ -611,9 +974,21 @@ fileField = Field
          case files of
              [] -> Right Nothing
              file:_ -> Right $ Just file
@@ -934,7 +931,7 @@ index b8109df..9bde340 100644
      , fieldEnctype = Multipart
      }
  
-@@ -638,10 +1015,20 @@ fileAFormReq fs = AForm $ \(site, langs) menvs ints -> do
+@@ -640,10 +1015,20 @@ fileAFormReq fs = AForm $ \(site, langs) menvs ints -> do
              { fvLabel = toHtml $ renderMessage site langs $ fsLabel fs
              , fvTooltip = fmap (toHtml . renderMessage site langs) $ fsTooltip fs
              , fvId = id'
@@ -959,7 +956,7 @@ index b8109df..9bde340 100644
              , fvErrors = errs
              , fvRequired = True
              }
-@@ -670,10 +1057,20 @@ fileAFormOpt fs = AForm $ \(master, langs) menvs ints -> do
+@@ -672,10 +1057,20 @@ fileAFormOpt fs = AForm $ \(master, langs) menvs ints -> do
              { fvLabel = toHtml $ renderMessage master langs $ fsLabel fs
              , fvTooltip = fmap (toHtml . renderMessage master langs) $ fsTooltip fs
              , fvId = id'
@@ -1770,7 +1767,7 @@ index 2862678..7b49b1a 100644
      }
    where
 diff --git a/yesod-form.cabal b/yesod-form.cabal
-index afd2de5..49fd684 100644
+index 39fa680..88ed066 100644
 --- a/yesod-form.cabal
 +++ b/yesod-form.cabal
 @@ -19,6 +19,7 @@ library
diff --git a/standalone/android/install-haskell-packages b/standalone/android/install-haskell-packages
index 318b850ba..f0a4b9113 100755
--- a/standalone/android/install-haskell-packages
+++ b/standalone/android/install-haskell-packages
@@ -50,7 +50,7 @@ patched () {
 
 installgitannexdeps () {
 	pushd ../..
-	echo cabal install --only-dependencies
+	echo cabal install --only-dependencies "$@"
 	cabal install --only-dependencies "$@"
 	popd
 }
@@ -90,11 +90,14 @@ install_pkgs () {
 	patched yesod-core
 	patched yesod-persistent
 	patched yesod-form
+	patched crypto-numbers
 	patched yesod-auth
 	patched yesod
 	patched async
 	patched gnuidn
 	patched DAV
+	patched language-javascript
+	patched uuid
 
 	cd ..
 
@@ -112,6 +115,6 @@ echo
 echo
 echo cross build
 echo
-PATH=$HOME/.ghc/android-14/arm-linux-androideabi-4.7/bin:$HOME/.ghc/android-14/arm-linux-androideabi-4.7/arm-linux-androideabi/bin:$PATH
+PATH=$HOME/.ghc/$(cat abiversion)/bin:$HOME/.ghc/$(cat abiversion)/arm-linux-androideabi/bin:$PATH
 cabal update
 install_pkgs
diff --git a/standalone/android/start b/standalone/android/start
new file mode 100755
index 000000000..44dcb3cf4
--- /dev/null
+++ b/standalone/android/start
diff --git a/standalone/windows/build.sh b/standalone/windows/build.sh
index 56aa58f31..74148dfe5 100644
--- a/standalone/windows/build.sh
+++ b/standalone/windows/build.sh
@@ -11,6 +11,8 @@ FLAGS="-Webapp -Assistant -XMPP"
 
 PATH="$HP/bin:$HP/lib/extralibs/bin:/c/Program Files (x86)/NSIS:$PATH"
 
+UPGRADE_LOCATION=http://downloads.kitenet.net/git-annex/windows/current/git-annex-installer.exe
+
 # Run a command with the cygwin environment available.
 # However, programs not from cygwin are preferred.
 withcyg () {