25 files changed, 376 insertions, 25 deletions
diff --git a/Annex/AutoMerge.hs b/Annex/AutoMerge.hs
index 92cccc004..f0f183dfb 100644
--- a/Annex/AutoMerge.hs
+++ b/Annex/AutoMerge.hs
@@ -134,7 +134,7 @@ resolveMerge' (Just us) them u = do
 	
 	makelink key = do
 		let dest = variantFile file key
-		l <- inRepo $ gitAnnexLink dest key
+		l <- calcRepo $ gitAnnexLink dest key
 		replacewithlink dest l
 		stageSymlink dest =<< hashSymlink l
 
diff --git a/Annex/Branch.hs b/Annex/Branch.hs
index 2191ec263..c67270312 100644
--- a/Annex/Branch.hs
+++ b/Annex/Branch.hs
@@ -49,9 +49,11 @@ import Annex.Perms
 import Logs
 import Logs.Transitions
 import Logs.Trust.Pure
+import Logs.Difference.Pure
 import Annex.ReplaceFile
 import qualified Annex.Queue
 import Annex.Branch.Transitions
+import qualified Annex
 
 {- Name of the branch that is used to store git-annex's information. -}
 name :: Git.Ref
@@ -160,6 +162,7 @@ updateTo pairs = do
 			<$> getLocal transitionsLog
 		unless (null branches) $ do
 			showSideAction merge_desc
+			mapM_ checkBranchDifferences refs
 			mergeIndex jl refs
 		let commitrefs = nub $ fullname:refs
 		unlessM (handleTransitions jl localtransitions commitrefs) $ do
@@ -537,3 +540,11 @@ performTransitionsLocked jl ts neednewlocalbranch transitionedrefs = do
 				apply rest hasher file content' trustmap
 			PreserveFile ->
 				apply rest hasher file content trustmap
+
+checkBranchDifferences :: Git.Ref -> Annex ()
+checkBranchDifferences ref = do
+	theirdiffs <- allDifferences . parseDifferencesLog . decodeBS
+		<$> catFile ref differenceLog
+	mydiffs <- annexDifferences <$> Annex.getGitConfig
+	when (theirdiffs /= mydiffs) $
+		error "Remote repository is tuned in incompatable way; cannot be merged with local repository."
diff --git a/Annex/Content.hs b/Annex/Content.hs
index 73f27fd28..a78cf674c 100644
--- a/Annex/Content.hs
+++ b/Annex/Content.hs
@@ -446,7 +446,7 @@ removeAnnex (ContentLock key) = withObjectLoc key remove removedirect
 		removeInodeCache key
 		mapM_ (resetfile cache) fs
 	resetfile cache f = whenM (sameInodeCache f cache) $ do
-		l <- inRepo $ gitAnnexLink f key
+		l <- calcRepo $ gitAnnexLink f key
 		secureErase f
 		replaceFile f $ makeAnnexLink l
 
diff --git a/Annex/Difference.hs b/Annex/Difference.hs
new file mode 100644
index 000000000..cb363e80c
--- /dev/null
+++ b/Annex/Difference.hs
@@ -0,0 +1,60 @@
+{- git-annex repository differences
+ -
+ - Copyright 2015 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Annex.Difference (
+	module Types.Difference,
+	setDifferences,
+) where
+
+import Common.Annex
+import Types.Difference
+import Logs.Difference
+import Config
+import Annex.UUID
+import Logs.UUID
+import Annex.Version
+import qualified Annex
+
+import qualified Data.Map as M
+
+-- Differences are only allowed to be tweaked when initializing a
+-- repository for the first time, and then only if there is not another
+-- known uuid. If the repository was cloned from elsewhere, it inherits
+-- the existing settings.
+--
+-- Must be called before setVersion, so it can check if this is the first
+-- time the repository is being initialized.
+setDifferences :: Annex ()
+setDifferences = do
+	u <- getUUID
+	otherds <- either error return 
+		=<< sanityCheckDifferences . allDifferences
+			<$> recordedDifferences
+	ds <- mappend otherds . annexDifferences <$> Annex.getGitConfig
+	when (ds /= mempty) $ do
+		ds'@(Differences l) <- ifM (isJust <$> getVersion)
+			( do
+				oldds <- recordedDifferencesFor u
+				when (ds /= oldds) $
+					warning $ "Cannot change tunable parameters in already initialized repository."
+				return oldds
+			, if otherds == mempty
+				then ifM (not . null . filter (/= u) . M.keys <$> uuidMap)
+					( do
+						warning "Cannot change tunable parameters in a clone of an existing repository."
+						return mempty
+					, return ds
+					)
+				else if otherds /= ds
+					then do
+						warning "The specified tunable parameters differ from values being used in other clones of this repository."
+						return otherds
+					else return ds
+			)
+		forM_ l $ \d ->
+			setConfig (ConfigKey $ differenceConfigKey d) (differenceConfigVal d)
+		recordDifferences ds' u
diff --git a/Annex/Direct.hs b/Annex/Direct.hs
index 06d0342c1..1c733cb55 100644
--- a/Annex/Direct.hs
+++ b/Annex/Direct.hs
@@ -86,7 +86,7 @@ stageDirect = do
 		deletegit file
 	
 	stageannexlink file key = do
-		l <- inRepo $ gitAnnexLink file key
+		l <- calcRepo $ gitAnnexLink file key
 		stageSymlink file =<< hashSymlink l
 		void $ addAssociatedFile key file
 
@@ -131,7 +131,7 @@ addDirect file cache = do
 		return False
 	got (Just (key, _)) = ifM (sameInodeCache file [cache])
 		( do
-			l <- inRepo $ gitAnnexLink file key
+			l <- calcRepo $ gitAnnexLink file key
 			stageSymlink file =<< hashSymlink l
 			addInodeCache key cache
 			void $ addAssociatedFile key file
@@ -282,7 +282,7 @@ updateWorkTree d oldref = do
 	 - with the content. -}
 	movein item makeabs k f = unlessM (goodContent k f) $ do
 		preserveUnannexed item makeabs f oldref
-		l <- inRepo $ gitAnnexLink f k
+		l <- calcRepo $ gitAnnexLink f k
 		replaceFile f $ makeAnnexLink l
 		toDirect k f
 	
diff --git a/Annex/Init.hs b/Annex/Init.hs
index 24c5e18b1..3f27a1172 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -27,6 +27,7 @@ import Logs.UUID
 import Logs.Trust.Basic
 import Types.TrustLevel
 import Annex.Version
+import Annex.Difference
 import Annex.UUID
 import Config
 import Annex.Direct
@@ -73,6 +74,7 @@ initialize' = do
 	checkCrippledFileSystem
 	unlessM isBare $
 		hookWrite preCommitHook
+	setDifferences
 	setVersion supportedVersion
 	ifM (crippledFileSystem <&&> not <$> isBare)
 		( do
diff --git a/Annex/View.hs b/Annex/View.hs
index 3a9168f6c..315cc7df2 100644
--- a/Annex/View.hs
+++ b/Annex/View.hs
@@ -354,7 +354,7 @@ applyView' mkviewedfile getfilemetadata view = do
 		let metadata' = getfilemetadata f `unionMetaData` metadata
 		forM_ (genviewedfiles f metadata') $ \fv -> do
 			f' <- fromRepo $ fromTopFilePath $ asTopFilePath fv
-			stagesymlink uh hasher f' =<< inRepo (gitAnnexLink f' k)
+			stagesymlink uh hasher f' =<< calcRepo (gitAnnexLink f' k)
 	go uh hasher f Nothing
 		| "." `isPrefixOf` f = do
 			s <- liftIO $ getSymbolicLinkStatus f
diff --git a/Assistant/Threads/Committer.hs b/Assistant/Threads/Committer.hs
index 2c1addb24..3f8debdc2 100644
--- a/Assistant/Threads/Committer.hs
+++ b/Assistant/Threads/Committer.hs
@@ -352,7 +352,7 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 	done change mcache file key = liftAnnex $ do
 		logStatus key InfoPresent
 		link <- ifM isDirect
-			( inRepo $ gitAnnexLink file key
+			( calcRepo $ gitAnnexLink file key
 			, Command.Add.link file key mcache
 			)
 		whenM (pure DirWatcher.eventsCoalesce <||> isDirect) $
diff --git a/Assistant/Threads/Watcher.hs b/Assistant/Threads/Watcher.hs
index ca9de6836..6f3afa8ca 100644
--- a/Assistant/Threads/Watcher.hs
+++ b/Assistant/Threads/Watcher.hs
@@ -232,7 +232,7 @@ onAddDirect symlinkssupported matcher file fs = do
 				 - so it symlink is restaged to make sure. -}
 				( ifM (shouldRestage <$> getDaemonStatus)
 					( do
-						link <- liftAnnex $ inRepo $ gitAnnexLink file key
+						link <- liftAnnex $ calcRepo $ gitAnnexLink file key
 						addLink file link (Just key)
 					, noChange
 					)
@@ -279,7 +279,7 @@ onAddSymlink' linktarget mk isdirect file filestatus = go mk
 	go (Just key) = do
 		when isdirect $
 			liftAnnex $ void $ addAssociatedFile key file
-		link <- liftAnnex $ inRepo $ gitAnnexLink file key
+		link <- liftAnnex $ calcRepo $ gitAnnexLink file key
 		if linktarget == Just link
 			then ensurestaged (Just link) =<< getDaemonStatus
 			else do
diff --git a/Command/Add.hs b/Command/Add.hs
index 2671126ca..51921fbc3 100644
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -230,7 +230,7 @@ undo file key e = do
 {- Creates the symlink to the annexed content, returns the link target. -}
 link :: FilePath -> Key -> Maybe InodeCache -> Annex String
 link file key mcache = flip catchNonAsync (undo file key) $ do
-	l <- inRepo $ gitAnnexLink file key
+	l <- calcRepo $ gitAnnexLink file key
 	replaceFile file $ makeAnnexLink l
 
 	-- touch symlink to have same time as the original file,
@@ -272,7 +272,7 @@ cleanup :: FilePath -> Key -> Maybe InodeCache -> Bool -> CommandCleanup
 cleanup file key mcache hascontent = do
 	ifM (isDirect <&&> pure hascontent)
 		( do
-			l <- inRepo $ gitAnnexLink file key
+			l <- calcRepo $ gitAnnexLink file key
 			stageSymlink file =<< hashSymlink l
 		, addLink file key mcache
 		)
diff --git a/Command/Fix.hs b/Command/Fix.hs
index 1ef15d0eb..c981d23ae 100644
--- a/Command/Fix.hs
+++ b/Command/Fix.hs
@@ -28,7 +28,7 @@ seek = withFilesInGit $ whenAnnexed start
 {- Fixes the symlink to an annexed file. -}
 start :: FilePath -> Key -> CommandStart
 start file key = do
-	link <- inRepo $ gitAnnexLink file key
+	link <- calcRepo $ gitAnnexLink file key
 	stopUnless ((/=) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file)) $ do
 		showStart "fix" file
 		next $ perform file link
diff --git a/Command/FromKey.hs b/Command/FromKey.hs
index 14a3d8176..d9ebe6b4c 100644
--- a/Command/FromKey.hs
+++ b/Command/FromKey.hs
@@ -33,7 +33,7 @@ start _ = error "specify a key and a dest file"
 
 perform :: Key -> FilePath -> CommandPerform
 perform key file = do
-	link <- inRepo $ gitAnnexLink file key
+	link <- calcRepo $ gitAnnexLink file key
 	liftIO $ createDirectoryIfMissing True (parentDir file)
 	liftIO $ createSymbolicLink link file
 	next $ cleanup file
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
index 46fe983d8..0242a1f75 100644
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -192,7 +192,7 @@ check cs = and <$> sequence cs
  -}
 fixLink :: Key -> FilePath -> Annex Bool
 fixLink key file = do
-	want <- inRepo $ gitAnnexLink file key
+	want <- calcRepo $ gitAnnexLink file key
 	have <- getAnnexLinkTarget file
 	maybe noop (go want) have
 	return True
diff --git a/Command/Indirect.hs b/Command/Indirect.hs
index 34a2ef8c9..1d703d2f3 100644
--- a/Command/Indirect.hs
+++ b/Command/Indirect.hs
@@ -88,7 +88,7 @@ perform = do
 			v <- tryNonAsync (moveAnnex k f)
 			case v of
 				Right _ -> do 
-					l <- inRepo $ gitAnnexLink f k
+					l <- calcRepo $ gitAnnexLink f k
 					liftIO $ createSymbolicLink l f
 				Left e -> catchNonAsync (Command.Add.undo f k e)
 					warnlocked
diff --git a/Locations.hs b/Locations.hs
index 596bf4f85..dcbde4bd9 100644
--- a/Locations.hs
+++ b/Locations.hs
@@ -76,6 +76,7 @@ import Common
 import Types
 import Types.Key
 import Types.UUID
+import Types.Difference
 import qualified Git
 
 {- Conventions:
@@ -120,17 +121,22 @@ annexLocation key hasher = objectDir </> keyPath key hasher
  - the actual location of the file's content.
  -}
 gitAnnexLocation :: Key -> Git.Repo -> GitConfig -> IO FilePath
-gitAnnexLocation key r config = gitAnnexLocation' key r (annexCrippledFileSystem config)
-gitAnnexLocation' :: Key -> Git.Repo -> Bool -> IO FilePath
-gitAnnexLocation' key r crippled
+gitAnnexLocation key r config = gitAnnexLocation' key r config (annexCrippledFileSystem config)
+gitAnnexLocation' :: Key -> Git.Repo -> GitConfig -> Bool -> IO FilePath
+gitAnnexLocation' key r config crippled
 	{- Bare repositories default to hashDirLower for new
 	 - content, as it's more portable.
 	 -
 	 - Repositories on filesystems that are crippled also use
 	 - hashDirLower, since they do not use symlinks and it's
-	 - more portable. -}
-	| Git.repoIsLocalBare r || crippled =
-		check $ map inrepo $ annexLocations key
+	 - more portable.
+	 -
+	 - ObjectHashLower can also be set to force it.
+	 -}
+	| Git.repoIsLocalBare r 
+		|| crippled 
+		|| hasDifference (== ObjectHashLower True) (annexDifferences config) =
+			check $ map inrepo $ annexLocations key
 	{- Non-bare repositories only use hashDirMixed, so
 	 - don't need to do any work to check if the file is
 	 - present. -}
@@ -141,11 +147,11 @@ gitAnnexLocation' key r crippled
 	check [] = error "internal"
 
 {- Calculates a symlink to link a file to an annexed object. -}
-gitAnnexLink :: FilePath -> Key -> Git.Repo -> IO FilePath
-gitAnnexLink file key r = do
+gitAnnexLink :: FilePath -> Key -> Git.Repo -> GitConfig -> IO FilePath
+gitAnnexLink file key r config = do
 	currdir <- getCurrentDirectory
 	let absfile = fromMaybe whoops $ absNormPathUnix currdir file
-	loc <- gitAnnexLocation' key r False
+	loc <- gitAnnexLocation' key r config False
 	relPathDirToFile (parentDir absfile) loc
   where
 	whoops = error $ "unable to normalize " ++ file
diff --git a/Logs.hs b/Logs.hs
index 7452339cd..8d8ae993b 100644
--- a/Logs.hs
+++ b/Logs.hs
@@ -39,6 +39,7 @@ topLevelUUIDBasedLogs =
 	, preferredContentLog
 	, requiredContentLog
 	, scheduleLog
+	, differenceLog
 	]
 
 {- All the ways to get a key from a presence log file -}
@@ -82,6 +83,9 @@ groupPreferredContentLog = "group-preferred-content.log"
 scheduleLog :: FilePath
 scheduleLog = "schedule.log"
 
+differenceLog :: FilePath
+differenceLog = "difference.log"
+
 {- The pathname of the location log file for a given key. -}
 locationLogFile :: Key -> String
 locationLogFile key = hashDirLower key ++ keyFile key ++ ".log"
diff --git a/Logs/Difference.hs b/Logs/Difference.hs
new file mode 100644
index 000000000..68d624f99
--- /dev/null
+++ b/Logs/Difference.hs
@@ -0,0 +1,40 @@
+{- git-annex difference log
+ -
+ - Copyright 2015 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Logs.Difference (
+	recordDifferences,
+	recordedDifferences,
+	recordedDifferencesFor,
+	module Logs.Difference.Pure
+) where
+
+import Data.Monoid
+import Data.Time.Clock.POSIX
+import qualified Data.Map as M
+
+import Common.Annex
+import Types.Difference
+import qualified Annex.Branch
+import Logs
+import Logs.UUIDBased
+import Logs.Difference.Pure
+
+recordDifferences :: Differences -> UUID -> Annex ()
+recordDifferences differences uuid = do
+	ts <- liftIO getPOSIXTime
+	Annex.Branch.change differenceLog $
+		showLog id . changeLog ts uuid (show differences) . parseLog Just
+
+-- Map of UUIDs that have Differences recorded.
+-- If a new version of git-annex has added a Difference this version
+-- doesn't know about, it will contain UnknownDifferences.
+recordedDifferences :: Annex (M.Map UUID Differences)
+recordedDifferences = parseDifferencesLog <$> Annex.Branch.get differenceLog
+
+recordedDifferencesFor :: UUID -> Annex Differences
+recordedDifferencesFor u = fromMaybe mempty . M.lookup u 
+	<$> recordedDifferences
diff --git a/Logs/Difference/Pure.hs b/Logs/Difference/Pure.hs
new file mode 100644
index 000000000..76d995a01
--- /dev/null
+++ b/Logs/Difference/Pure.hs
@@ -0,0 +1,26 @@
+{- git-annex difference log, pure functions
+ -
+ - Copyright 2015 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Logs.Difference.Pure (
+	allDifferences,
+	parseDifferencesLog,
+) where
+
+import Data.Monoid
+import qualified Data.Map as M
+
+import Common.Annex
+import Types.Difference
+import Logs.UUIDBased
+
+parseDifferencesLog :: String -> (M.Map UUID Differences)
+parseDifferencesLog = simpleMap 
+	. parseLog (Just . fromMaybe UnknownDifferences . readish)
+
+-- The sum of all recorded differences, across all UUIDs.
+allDifferences :: M.Map UUID Differences -> Differences
+allDifferences = mconcat . M.elems
diff --git a/Types/Difference.hs b/Types/Difference.hs
new file mode 100644
index 000000000..cbfad0fce
--- /dev/null
+++ b/Types/Difference.hs
@@ -0,0 +1,135 @@
+{- git-annex repository differences
+ -
+ - Copyright 2015 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Types.Difference (
+	Difference(..),
+	Differences(..),
+	getDifferences,
+	sanityCheckDifferences,
+	differenceConfigKey,
+	differenceConfigVal,
+	hasDifference,
+) where
+
+import Utility.PartialPrelude
+import qualified Git
+import qualified Git.Config
+
+import Data.List
+import Data.Maybe
+import Data.Monoid
+import Control.Applicative
+
+-- Describes differences from the v5 repository format.
+--
+-- The serilization is stored in difference.log, so avoid changes that
+-- would break compatability.
+--
+-- Not breaking comparability is why a list of Differences is used, rather
+-- than a sum type. With a sum type, adding a new field for some future
+-- difference would serialize to a value that an older version could not
+-- parse, even if that new field was not used. With the Differences list,
+-- old versions can still parse it, unless the new Difference constructor 
+-- is used.
+data Difference
+	= Version Int
+	| ObjectHashLower Bool
+	| ObjectHashDirectories Int
+	| BranchHashDirectories Int
+	deriving (Show, Read, Ord)
+
+instance Eq Difference where
+	Version a == Version b = a == b
+	ObjectHashLower a == ObjectHashLower b = a == b
+	ObjectHashDirectories a == ObjectHashDirectories b = a == b
+	BranchHashDirectories a == BranchHashDirectories b = a == b
+	_ == _ = False
+
+data Differences
+	= Differences [Difference]
+	| UnknownDifferences
+	deriving (Show, Read, Ord)
+
+instance Eq Differences where
+	Differences a == Differences b = simplify (defver:a) == simplify (defver:b)
+	_ == _ = False
+
+instance Monoid Differences where
+	mempty = Differences []
+	mappend (Differences l1) (Differences l2) = Differences (simplify (l1 ++ l2))
+	mappend _ _ = UnknownDifferences
+
+-- This is the default repository version that is assumed when no other one
+-- is given. Note that [] == [Version 5]
+defver :: Difference
+defver = Version 5
+
+-- Larger values of the same Difference constructor dominate
+-- over smaller values, so given [Version 6, Version 5], returns [Version 6]
+simplify :: [Difference] -> [Difference]
+simplify = go . sort
+  where
+	go [] = []
+	go (d:[]) = [d]
+	go (d1:d2:ds)
+		| like d1 d2 = go (d2:ds)
+		| otherwise = d1 : go (d2:ds)
+
+	like (Version _) (Version _) = True
+	like (ObjectHashLower _) (ObjectHashLower _) = True
+	like (ObjectHashDirectories _) (ObjectHashDirectories _) = True
+	like (BranchHashDirectories _) (BranchHashDirectories _) = True
+	like _ _ = False
+
+getDifferences :: Git.Repo -> Differences
+getDifferences r = checksane $ Differences $ catMaybes
+	[ ObjectHashLower 
+		<$> getmaybebool (differenceConfigKey (ObjectHashLower undefined))
+	, ObjectHashDirectories 
+		<$> getmayberead (differenceConfigKey (ObjectHashDirectories undefined))
+	, BranchHashDirectories
+		<$> getmayberead (differenceConfigKey (BranchHashDirectories undefined))
+	]
+  where
+	getmaybe k = Git.Config.getMaybe k r
+	getmayberead k = readish =<< getmaybe k
+	getmaybebool k = Git.Config.isTrue =<< getmaybe k
+	checksane = either error id . sanityCheckDifferences
+
+differenceConfigKey :: Difference -> String
+differenceConfigKey (Version _) = "annex.version"
+differenceConfigKey (ObjectHashLower _) = tunable "objecthashlower"
+differenceConfigKey (ObjectHashDirectories _) = tunable "objecthashdirectories"
+differenceConfigKey (BranchHashDirectories _) = tunable "branchhashdirectories"
+
+differenceConfigVal :: Difference -> String
+differenceConfigVal (Version v) = show v
+differenceConfigVal (ObjectHashLower b) = Git.Config.boolConfig b
+differenceConfigVal (ObjectHashDirectories n) = show n
+differenceConfigVal (BranchHashDirectories n) = show n
+
+tunable :: String -> String
+tunable k = "annex.tune." ++ k
+
+sanityCheckDifferences :: Differences -> Either String Differences
+sanityCheckDifferences d@(Differences l)
+	| null problems = Right d
+	| otherwise = Left (intercalate "; " problems)
+  where
+	problems = catMaybes (map check l)
+	check (ObjectHashDirectories n)
+		| n == 1 || n == 2 = Nothing
+		| otherwise = Just $ "Bad value for objecthashdirectories -- should be 1 or 2, not " ++ show n
+	check (BranchHashDirectories n)
+		| n == 1 || n == 2 = Nothing
+		| otherwise = Just $ "Bad value for branhhashdirectories -- should be 1 or 2, not " ++ show n
+	check _ = Nothing
+sanityCheckDifferences UnknownDifferences = Left "unknown differences detected; update git-annex"
+
+hasDifference :: (Difference -> Bool) -> Differences -> Bool
+hasDifference f (Differences l) = any f l
+hasDifference _ UnknownDifferences = False
diff --git a/Types/GitConfig.hs b/Types/GitConfig.hs
index ef8068cc4..5ac524f45 100644
--- a/Types/GitConfig.hs
+++ b/Types/GitConfig.hs
@@ -20,6 +20,7 @@ import Config.Cost
 import Types.Distribution
 import Types.Availability
 import Types.NumCopies
+import Types.Difference
 import Utility.HumanTime
 
 {- Main git-annex settings. Each setting corresponds to a git-config key
@@ -56,6 +57,7 @@ data GitConfig = GitConfig
 	, annexHardLink :: Bool
 	, coreSymlinks :: Bool
 	, gcryptId :: Maybe String
+	, annexDifferences :: Differences
 	}
 
 extractGitConfig :: Git.Repo -> GitConfig
@@ -93,6 +95,7 @@ extractGitConfig r = GitConfig
 	, annexHardLink = getbool (annex "hardlink") False
 	, coreSymlinks = getbool "core.symlinks" True
 	, gcryptId = getmaybe "core.gcrypt-id"
+	, annexDifferences = getDifferences r
 	}
   where
 	getbool k def = fromMaybe def $ getmaybebool k
diff --git a/Upgrade/V1.hs b/Upgrade/V1.hs
index 1f0dae43e..e8a7efe13 100644
--- a/Upgrade/V1.hs
+++ b/Upgrade/V1.hs
@@ -92,7 +92,7 @@ updateSymlinks = do
 		case r of
 			Nothing -> noop
 			Just (k, _) -> do
-				link <- inRepo $ gitAnnexLink f k
+				link <- calcRepo $ gitAnnexLink f k
 				liftIO $ removeFile f
 				liftIO $ createSymbolicLink link f
 				Annex.Queue.addCommand "add" [Param "--"] [f]
diff --git a/debian/changelog b/debian/changelog
index 0e028afc2..3caa7ddad 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -21,6 +21,11 @@ git-annex (5.20150114) UNRELEASED; urgency=medium
     with an existing file. (--file overrides this)
   * Fix default repository description created by git annex init,
     which got broken by the relative path changes in the last release.
+  * init: Repository tuning parameters can now be passed when initializing a
+    repository for the first time. For details, see
+    http://git-annex.branchable.com/tuning/
+  * merge: Refuse to merge changes from a git-annex branch of a repo
+    that has been tuned in incompatable ways.
 
  -- Joey Hess <id@joeyh.name>  Tue, 13 Jan 2015 17:03:39 -0400
 
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index c4586ba1d..06eb85e11 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -1839,6 +1839,12 @@ Here are all the supported configuration settings.
   Used by hook special remotes and external special remotes to record
   the type of the remote.
 
+* `annex.tune.objecthashdirectories`, `annex.tune.objecthashlower`, `annex.tune.branchhashdirectories`
+
+  These can be passed to `git annex init` to tune the repository.
+  They cannot be safely changed in a running repository.
+  For details, see <http://git-annex.branchable.com/tuning/>.
+
 # CONFIGURATION VIA .gitattributes
 
 The key-value backend used when adding a new file to the annex can be
diff --git a/doc/internals.mdwn b/doc/internals.mdwn
index b8cb559b6..4eb72ceac 100644
--- a/doc/internals.mdwn
+++ b/doc/internals.mdwn
@@ -257,3 +257,12 @@ Example:
 
 	ForgetGitHistory 1387325539.685136s
 	ForgetDeadRemotes 1387325539.685136s
+
+## `difference.log`
+
+Used when a repository has fundamental differences from other repositories,
+that should prevent merging.
+
+Example:
+
+	e605dca6-446a-11e0-8b2a-002170d25c55 [Version 5] timestamp=1422387398.30395s
diff --git a/doc/tuning.mdwn b/doc/tuning.mdwn
new file mode 100644
index 000000000..761071b6b
--- /dev/null
+++ b/doc/tuning.mdwn
@@ -0,0 +1,44 @@
+git-annex now has experimental support for tuning a repository for
+different work loads. 
+
+For example, a repository with a very large number of files in it may work
+better if git-annex uses some nonstandard hash format, for either the
+`.git/annex/objects/` directory, or for the log files in the git-annex
+branch.
+
+A repository can currently only be tuned when it is first created; this is
+done by passing `-c name=value` parameters to `git annex init`.
+
+For example, this will make git-annex use only 1 level for hash directories
+in `.git/annex/objects`:
+
+	git -c annex.tune.objecthashdirectories=1 annex init
+
+It's very important to keep in mind that this makes a nonstandard format
+git-annex repository. In general, this cannot safely be used with
+git-annex older than version 5.20150128. Older version of git-annex will
+not understand and will get confused and perhaps do bad things.
+
+Also, it's not safe to merge two separate git repositories that have been
+tuned differently (or one tuned and the other one not). git-annex will
+prevent merging their git-annex branches together, but it cannot prevent
+`git merge remote/master` merging two branches, and the result will be ugly
+at best (`git annex fix` can fix up the mess somewhat).
+
+Again, tuned repositories are an experimental feature; use with caution!
+
+The following tuning parameters are available:
+
+* `annex.tune.objecthashdirectories` (default: 2)  
+  Sets the number of hash directories to use in `.git/annex/objects/`
+
+* `annex.tune.objecthashlower` (default: false)
+  Set to true to make the hash directories in `.git/annex/objects/` use
+  all lower-case.
+
+* `annex.tune.branchhashdirectories` (default: 2)
+  Sets the number of hash directories to use in the git-annex branch.
+
+Note that git-annex will automatically propigate these setting to
+`.git/config` for tuned repsitories. You should never directly change
+these settings in `.git/config`