Fix direct mode getKeysPresent false positive & also sped up direct mode unused and unannex

unused: In direct mode, files that are deleted from the work tree are no longer incorrectly detected as unused.

Direct mode `git annex info` slows down a bit due to more stringent
checking, but not by a lot.

7 files changed, 52 insertions, 18 deletions

diff --git a/Annex/Content.hs b/Annex/Content.hs
index 740ed8bbc..9c71037de 100644
--- a/Annex/Content.hs
+++ b/Annex/Content.hs
@@ -24,6 +24,7 @@ module Annex.Content (
 	removeAnnex,
 	fromAnnex,
 	moveBad,
+	KeyLocation(..),
 	getKeysPresent,
 	saveState,
 	downloadUrl,
@@ -466,22 +467,33 @@ moveBad key = do
 	logStatus key InfoMissing
 	return dest
 
-{- List of keys whose content exists in the annex. -}
-getKeysPresent :: Annex [Key]
-getKeysPresent = do
+data KeyLocation = InAnnex | InRepository
+
+{- List of keys whose content exists in the specified location.
+ 
+ - InAnnex only lists keys under .git/annex/objects,
+ - while InRepository, in direct mode, also finds keys located in the
+ - work tree.
+ -
+ - Note that InRepository has to check whether direct mode files
+ - have goodContent.
+ -}
+getKeysPresent :: KeyLocation -> Annex [Key]
+getKeysPresent keyloc = do
 	direct <- isDirect
 	dir <- fromRepo gitAnnexObjectDir
-	liftIO $ traverse direct (2 :: Int) dir
+	s <- getstate direct
+	liftIO $ traverse s direct (2 :: Int) dir
   where
-	traverse direct depth dir = do
+	traverse s direct depth dir = do
 		contents <- catchDefaultIO [] (dirContents dir)
 		if depth == 0
 			then do
-				contents' <- filterM (present direct) contents
+				contents' <- filterM (present s direct) contents
 				let keys = mapMaybe (fileKey . takeFileName) contents'
 				continue keys []
 			else do
-				let deeper = traverse direct (depth - 1)
+				let deeper = traverse s direct (depth - 1)
 				continue [] (map deeper contents)
 	continue keys [] = return keys
 	continue keys (a:as) = do
@@ -489,15 +501,31 @@ getKeysPresent = do
 		morekeys <- unsafeInterleaveIO a
 		continue (morekeys++keys) as
 
-	{- In indirect mode, look for the key. In direct mode,
-	 - the inode cache file is only present when a key's content
-	 - is present, so can be used as a surrogate if the content
-	 - is not located in the annex directory. -}
-	present False d = doesFileExist $ contentfile d
-	present True d = doesFileExist (contentfile d ++ ".cache")
-		<||> present False d
+	present _ False d = presentInAnnex d
+	present s True d = presentDirect s d <||> presentInAnnex d
+
+	presentInAnnex = doesFileExist . contentfile
 	contentfile d = d </> takeFileName d
 
+	presentDirect s d = case keyloc of
+		InAnnex -> return False
+		InRepository -> case fileKey (takeFileName d) of
+			Nothing -> return False
+			Just k -> Annex.eval s $ 
+				anyM (goodContent k) =<< associatedFiles k
+
+	{- In order to run Annex monad actions within unsafeInterleaveIO,
+	 - the current state is taken and reused. No changes made to this
+	 - state will be preserved. 
+	 -
+	 - As an optimsation, call inodesChanged to prime the state with
+	 - a cached value that will be used in the call to goodContent.
+	 -}
+	getstate direct = do
+		when direct $
+			void $ inodesChanged
+		Annex.getState id
+
 {- Things to do to record changes to content when shutting down.
  -
  - It's acceptable to avoid committing changes to the branch,
diff --git a/Annex/Init.hs b/Annex/Init.hs
index 57379535d..e095aef61 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -198,7 +198,7 @@ enableDirectMode = unlessM isDirect $ do
  -}
 fixBadBare :: Annex ()
 fixBadBare = whenM checkBadBare $ do
-	ks <- getKeysPresent
+	ks <- getKeysPresent InAnnex
 	liftIO $ debugM "Init" $ unwords
 		[ "Detected bad bare repository with"
 		, show (length ks)
diff --git a/Command/Info.hs b/Command/Info.hs
index f27fdfb1d..11ed98cd9 100644
--- a/Command/Info.hs
+++ b/Command/Info.hs
@@ -281,7 +281,7 @@ cachedPresentData = do
 	case presentData s of
 		Just v -> return v
 		Nothing -> do
-			v <- foldKeys <$> lift getKeysPresent
+			v <- foldKeys <$> lift (getKeysPresent InRepository)
 			put s { presentData = Just v }
 			return v
 
diff --git a/Command/Uninit.hs b/Command/Uninit.hs
index 1c8d08689..2a9e3e687 100644
--- a/Command/Uninit.hs
+++ b/Command/Uninit.hs
@@ -53,7 +53,7 @@ finish :: Annex ()
 finish = do
 	annexdir <- fromRepo gitAnnexDir
 	annexobjectdir <- fromRepo gitAnnexObjectDir
-	leftovers <- removeUnannexed =<< getKeysPresent
+	leftovers <- removeUnannexed =<< getKeysPresent InAnnex
 	if null leftovers
 		then liftIO $ removeDirectoryRecursive annexdir
 		else error $ unlines
diff --git a/Command/Unused.hs b/Command/Unused.hs
index 6b4475568..c174cd256 100644
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -71,7 +71,9 @@ checkUnused = chain 0
 		return []
 	findunused False = do
 		showAction "checking for unused data"
-		excludeReferenced =<< getKeysPresent
+		-- InAnnex, not InRepository because if a direct mode
+		-- file exists, it is obviously not unused.
+		excludeReferenced =<< getKeysPresent InAnnex
 	chain _ [] = next $ return True
 	chain v (a:as) = do
 		v' <- a v
diff --git a/debian/changelog b/debian/changelog
index b33f4c9cd..26153c5fd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,8 @@ git-annex (5.20140307) UNRELEASED; urgency=medium
   * Fix zombie leak and general inneficiency when copying files to a
     local git repo.
   * webapp: Added a "Sync now" item to each repository's menu.
+  * unused: In direct mode, files that are deleted from the work tree
+    are no longer incorrectly detected as unused.
 
  -- Joey Hess <joeyh@debian.org>  Thu, 06 Mar 2014 16:17:01 -0400
 
diff --git a/doc/bugs/copy_unused_and_unused_not_agreeing.mdwn b/doc/bugs/copy_unused_and_unused_not_agreeing.mdwn
index 68328ac96..3790a0edf 100644
--- a/doc/bugs/copy_unused_and_unused_not_agreeing.mdwn
+++ b/doc/bugs/copy_unused_and_unused_not_agreeing.mdwn
@@ -46,3 +46,5 @@ copy SHA256E-s293288--30f1367fc326f7b053012818863151206f9e3ddeab3c3fc5b5c1c573d1
 copy SHA256E-s3672986--be960f6dc247df2496f634f7d788bd4a180fe556230e2dafc23ebc8fc1f10af3.JPG (checking synology...) ok
 $
 """]]
+
+> [[fixed|done]] per my comment --[[Joey]]