Use lower case hash directories for storing files on crippled filesystems, same as is already done for bare repositories.

* since this is a crippled filesystem anyway, git-annex doesn't use
  symlinks on it
* so there's no reason to use the mixed case hash directories that we're
  stuck using to avoid breaking everyone's symlinks to the content
* so we can do what is already done for all bare repos, and make non-bare
  repos on crippled filesystems use the all-lower case hash directories
* which are, happily, all 3 letters long, so they cannot conflict with
  mixed case hash directories
* so I was able to 100% fix this and even resuming `git annex add` in the
  test case will recover and it will all just work.

Annex.hs

@@ -28,6 +28,7 @@ module Annex (
 	gitRepo,
 	inRepo,
 	fromRepo,
+	calcRepo,
 	getGitConfig,
 	changeGitConfig,
 	changeGitRepo,
@@ -203,6 +204,11 @@ inRepo a = liftIO . a =<< gitRepo
 fromRepo :: (Git.Repo -> a) -> Annex a
 fromRepo a = a <$> gitRepo
 
+calcRepo :: (Git.Repo -> GitConfig -> IO a) -> Annex a
+calcRepo a = do
+	s <- getState id
+	liftIO $ a (repo s) (gitconfig s)
+
 {- Gets the GitConfig settings. -}
 getGitConfig :: Annex GitConfig
 getGitConfig = getState gitconfig

Annex/Content.hs

@@ -9,7 +9,6 @@ module Annex.Content (
 	inAnnex,
 	inAnnexSafe,
 	lockContent,
-	calcGitLink,
 	getViaTmp,
 	getViaTmpChecked,
 	getViaTmpUnchecked,
@@ -101,7 +100,7 @@ inAnnexSafe = inAnnex' (fromMaybe False) (Just False) go
  - it. (If the content is not present, no locking is done.) -}
 lockContent :: Key -> Annex a -> Annex a
 lockContent key a = do
-	file <- inRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
 	bracketIO (openforlock file >>= lock) unlock a
   where
 	{- Since files are stored with the write bit disabled, have
@@ -123,16 +122,6 @@ lockContent key a = do
 	unlock Nothing = noop
 	unlock (Just l) = closeFd l
 
-{- Calculates the relative path to use to link a file to a key. -}
-calcGitLink :: FilePath -> Key -> Annex FilePath
-calcGitLink file key = do
-	cwd <- liftIO getCurrentDirectory
-	let absfile = fromMaybe whoops $ absNormPath cwd file
-	loc <- inRepo $ gitAnnexLocation key
-	return $ relPathDirToFile (parentDir absfile) loc
-  where
-	whoops = error $ "unable to normalize " ++ file
-
 {- Runs an action, passing it a temporary filename to get,
  - and if the action succeeds, moves the temp file into 
  - the annex as a key's content. -}
@@ -251,7 +240,7 @@ moveAnnex key src = withObjectLoc key storeobject storedirect
 	storedirect fs = storedirect' =<< filterM validsymlink fs
 	validsymlink f = (==) (Just key) <$> isAnnexLink f
 
-	storedirect' [] = storeobject =<< inRepo (gitAnnexLocation key)
+	storedirect' [] = storeobject =<< calcRepo (gitAnnexLocation key)
 	storedirect' (dest:fs) = do
 		updateInodeCache key src
 		thawContent src
@@ -341,11 +330,11 @@ withObjectLoc key indirect direct = ifM isDirect
 	, goindirect
 	)
   where
-	goindirect = indirect =<< inRepo (gitAnnexLocation key)
+	goindirect = indirect =<< calcRepo (gitAnnexLocation key)
 
 cleanObjectLoc :: Key -> Annex ()
 cleanObjectLoc key = do
-	file <- inRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
 	unlessM crippledFileSystem $
 		void $ liftIO $ catchMaybeIO $ allowWrite $ parentDir file
 	liftIO $ removeparents file (3 :: Int)
@@ -374,7 +363,7 @@ removeAnnex key = withObjectLoc key remove removedirect
 		removeInodeCache key
 		mapM_ (resetfile cache) fs
 	resetfile cache f = whenM (sameInodeCache f cache) $ do
-		l <- calcGitLink f key
+		l <- inRepo $ gitAnnexLink f key
 		top <- fromRepo Git.repoPath
 		cwd <- liftIO getCurrentDirectory
 		let top' = fromMaybe top $ absNormPath cwd top
@@ -384,7 +373,7 @@ removeAnnex key = withObjectLoc key remove removedirect
 {- Moves a key's file out of .git/annex/objects/ -}
 fromAnnex :: Key -> FilePath -> Annex ()
 fromAnnex key dest = do
-	file <- inRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
 	unlessM crippledFileSystem $
 		liftIO $ allowWrite $ parentDir file
 	thawContent file
@@ -395,7 +384,7 @@ fromAnnex key dest = do
  - returns the file it was moved to. -}
 moveBad :: Key -> Annex FilePath
 moveBad key = do
-	src <- inRepo $ gitAnnexLocation key
+	src <- calcRepo $ gitAnnexLocation key
 	bad <- fromRepo gitAnnexBadDir
 	let dest = bad </> takeFileName src
 	createAnnexDirectory (parentDir dest)
@@ -468,7 +457,7 @@ preseedTmp key file = go =<< inAnnex key
 	copy = ifM (liftIO $ doesFileExist file)
 		( return True
 		, do
-			s <- inRepo $ gitAnnexLocation key
+			s <- calcRepo $ gitAnnexLocation key
 			liftIO $ copyFileExternal s file
 		)
 

Annex/Content/Direct.hs

@@ -42,7 +42,7 @@ associatedFiles key = do
  - the top of the repo. -}
 associatedFilesRelative :: Key -> Annex [FilePath] 
 associatedFilesRelative key = do
-	mapping <- inRepo $ gitAnnexMapping key
+	mapping <- calcRepo $ gitAnnexMapping key
 	liftIO $ catchDefaultIO [] $ do
 		h <- openFile mapping ReadMode
 		fileEncoding h
@@ -52,7 +52,7 @@ associatedFilesRelative key = do
  - transformation to the list. Returns new associatedFiles value. -}
 changeAssociatedFiles :: Key -> ([FilePath] -> [FilePath]) -> Annex [FilePath]
 changeAssociatedFiles key transform = do
-	mapping <- inRepo $ gitAnnexMapping key
+	mapping <- calcRepo $ gitAnnexMapping key
 	files <- associatedFilesRelative key
 	let files' = transform files
 	when (files /= files') $ do
@@ -124,7 +124,7 @@ removeInodeCache key = withInodeCacheFile key $ \f -> do
 	liftIO $ nukeFile f
 
 withInodeCacheFile :: Key -> (FilePath -> Annex a) -> Annex a
-withInodeCacheFile key a = a =<< inRepo (gitAnnexInodeCache key)
+withInodeCacheFile key a = a =<< calcRepo (gitAnnexInodeCache key)
 
 {- Checks if a InodeCache matches the current version of a file. -}
 sameInodeCache :: FilePath -> Maybe InodeCache -> Annex Bool

Annex/Direct.hs

@@ -89,7 +89,8 @@ addDirect file cache = do
 		return False
 	got (Just (key, _)) = ifM (sameInodeCache file $ Just cache)
 		( do
-			stageSymlink file =<< hashSymlink =<< calcGitLink file key
+			l <- inRepo $ gitAnnexLink file key
+			stageSymlink file =<< hashSymlink l
 			writeInodeCache key cache
 			void $ addAssociatedFile key file
 			logStatus key InfoPresent
@@ -152,7 +153,7 @@ mergeDirectCleanup d oldsha newsha = do
 	 -
  	 - Symlinks are replaced with their content, if it's available. -}
 	movein k f = do
-		l <- calcGitLink f k
+		l <- inRepo $ gitAnnexLink f k
 		replaceFile f $ makeAnnexLink l
 		toDirect k f
 	
@@ -169,7 +170,7 @@ toDirect k f = fromMaybe noop =<< toDirectGen k f
 
 toDirectGen :: Key -> FilePath -> Annex (Maybe (Annex ()))
 toDirectGen k f = do
-	loc <- inRepo $ gitAnnexLocation k
+	loc <- calcRepo $ gitAnnexLocation k
 	absf <- liftIO $ absPath f
 	locs <- filter (/= absf) <$> addAssociatedFile k f
 	case locs of

Assistant/Threads/Committer.hs

@@ -312,7 +312,7 @@ handleAdds delayadd cs = returnWhen (null incomplete) $ do
 	done change file key = liftAnnex $ do
 		logStatus key InfoPresent
 		link <- ifM isDirect
-			( calcGitLink file key
+			( inRepo $ gitAnnexLink file key
 			, Command.Add.link file key True
 			)
 		whenM (pure DirWatcher.eventsCoalesce <||> isDirect) $ do

Assistant/Threads/Watcher.hs

@@ -201,7 +201,7 @@ onAddDirect matcher file fs = do
 				 - just been deleted and been put back,
 				 - so it symlink is restaged to make sure. -}
 				( do
-					link <- liftAnnex $ calcGitLink file key
+					link <- liftAnnex $ inRepo $ gitAnnexLink file key
 					addLink file link (Just key)
 				, do
 					debug ["changed direct", file]
@@ -222,7 +222,7 @@ onAddSymlink isdirect file filestatus = go =<< liftAnnex (Backend.lookupFile fil
 	go (Just (key, _)) = do
 		when isdirect $
 			liftAnnex $ void $ addAssociatedFile key file
-		link <- liftAnnex $ calcGitLink file key
+		link <- liftAnnex $ inRepo $ gitAnnexLink file key
 		ifM ((==) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file))
 			( ensurestaged (Just link) (Just key) =<< getDaemonStatus
 			, do

Command/Add.hs

@@ -168,13 +168,13 @@ undo file key e = do
 	-- fromAnnex could fail if the file ownership is weird
 	tryharder :: IOException -> Annex ()
 	tryharder _ = do
-		src <- inRepo $ gitAnnexLocation key
+		src <- calcRepo $ gitAnnexLocation key
 		liftIO $ moveFile src file
 
 {- Creates the symlink to the annexed content, returns the link target. -}
 link :: FilePath -> Key -> Bool -> Annex String
 link file key hascontent = handle (undo file key) $ do
-	l <- calcGitLink file key
+	l <- inRepo $ gitAnnexLink file key
 	replaceFile file $ makeAnnexLink l
 
 #ifndef __ANDROID__
@@ -206,7 +206,9 @@ cleanup file key hascontent = do
 	when hascontent $
 		logStatus key InfoPresent
 	ifM (isDirect <&&> pure hascontent)
-		( stageSymlink file =<< hashSymlink =<< calcGitLink file key
+		( do
+			l <- inRepo $ gitAnnexLink file key
+			stageSymlink file =<< hashSymlink l
 		, ifM (coreSymlinks <$> Annex.getGitConfig)
 			( do
 				_ <- link file key hascontent

Command/Fix.hs

@@ -10,7 +10,6 @@ module Command.Fix where
 import Common.Annex
 import Command
 import qualified Annex.Queue
-import Annex.Content
 
 def :: [Command]
 def = [notDirect $ noCommit $ command "fix" paramPaths seek
@@ -22,7 +21,7 @@ seek = [withFilesInGit $ whenAnnexed start]
 {- Fixes the symlink to an annexed file. -}
 start :: FilePath -> (Key, Backend) -> CommandStart
 start file (key, _) = do
-	link <- calcGitLink file key
+	link <- inRepo $ gitAnnexLink file key
 	stopUnless ((/=) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file)) $ do
 		showStart "fix" file
 		next $ perform file link

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 <- calcGitLink file key
+	link <- inRepo $ gitAnnexLink file key
 	liftIO $ createDirectoryIfMissing True (parentDir file)
 	liftIO $ createSymbolicLink link file
 	next $ cleanup file

Command/Fsck.hs

@@ -188,7 +188,7 @@ check cs = all id <$> sequence cs
  -}
 fixLink :: Key -> FilePath -> Annex Bool
 fixLink key file = do
-	want <- calcGitLink file key
+	want <- inRepo $ gitAnnexLink file key
 	have <- getAnnexLinkTarget file
 	maybe noop (go want) have
 	return True
@@ -223,7 +223,7 @@ 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 <- inRepo $ gitAnnexLocation key
+		file <- calcRepo $ gitAnnexLocation key
 		freezeContent file
 		freezeContentDir file
 
@@ -281,7 +281,7 @@ checkKeySize :: Key -> Annex Bool
 checkKeySize key = ifM isDirect
 	( return True
 	, do
-		file <- inRepo $ gitAnnexLocation key
+		file <- calcRepo $ gitAnnexLocation key
 		ifM (liftIO $ doesFileExist file)
 			( checkKeySizeOr badContent key file
 			, return True
@@ -322,7 +322,7 @@ checkKeySizeOr bad key file = case Types.Key.keySize key of
  -}
 checkBackend :: Backend -> Key -> Annex Bool
 checkBackend backend key = do
-	file <- inRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
 	ifM isDirect
 		( ifM (goodContent key file)
 			( checkBackendOr' (badContentDirect file) backend key file
@@ -443,14 +443,14 @@ needFsck _ _ = return True
  -}
 recordFsckTime :: Key -> Annex ()
 recordFsckTime key = do
-	parent <- parentDir <$> inRepo (gitAnnexLocation key)
+	parent <- parentDir <$> calcRepo (gitAnnexLocation key)
 	liftIO $ void $ tryIO $ do
 		touchFile parent
 		setSticky parent
 
 getFsckTime :: Key -> Annex (Maybe EpochTime)
 getFsckTime key = do
-	parent <- parentDir <$> inRepo (gitAnnexLocation key)
+	parent <- parentDir <$> calcRepo (gitAnnexLocation key)
 	liftIO $ catchDefaultIO Nothing $ do
 		s <- getFileStatus parent
 		return $ if isSticky $ fileMode s

Command/Indirect.hs

@@ -82,13 +82,13 @@ perform = do
 		cleandirect k -- clean before content directory gets frozen
 		whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
 			moveAnnex k f
-			l <- calcGitLink f k
+			l <- inRepo $ gitAnnexLink f k
 			liftIO $ createSymbolicLink l f
 		showEndOk
 
 	cleandirect k = do
-		liftIO . nukeFile =<< inRepo (gitAnnexInodeCache k)
+		liftIO . nukeFile =<< calcRepo (gitAnnexInodeCache k)
-		liftIO . nukeFile =<< inRepo (gitAnnexMapping k)
+		liftIO . nukeFile =<< calcRepo (gitAnnexMapping k)
 
 cleanup :: CommandCleanup
 cleanup = do

Command/Migrate.hs

@@ -63,7 +63,7 @@ perform file oldkey oldbackend newbackend = do
 	go newkey = stopUnless (Command.ReKey.linkKey oldkey newkey) $
 		next $ Command.ReKey.cleanup file oldkey newkey
 	genkey = do
-		content <- inRepo $ gitAnnexLocation oldkey
+		content <- calcRepo $ gitAnnexLocation oldkey
 		let source = KeySource
 			{ keyFilename = file
 			, contentLocation = content

Command/ReKey.hs

@@ -49,7 +49,7 @@ perform file oldkey newkey = do
 {- Make a hard link to the old key content, to avoid wasting disk space. -}
 linkKey :: Key -> Key -> Annex Bool
 linkKey oldkey newkey = getViaTmpUnchecked newkey $ \tmp -> do
-	src <- inRepo $ gitAnnexLocation oldkey
+	src <- calcRepo $ gitAnnexLocation oldkey
 	ifM (liftIO $ doesFileExist tmp)
 		( return True
 		, ifM crippledFileSystem

Command/Sync.hs

@@ -14,7 +14,6 @@ import qualified Remote
 import qualified Annex
 import qualified Annex.Branch
 import qualified Annex.Queue
-import Annex.Content
 import Annex.Direct
 import Annex.CatFile
 import Annex.Link
@@ -268,7 +267,7 @@ resolveMerge' u
 		[Just SymlinkBlob, Nothing]
 	makelink (Just key) = do
 		let dest = mergeFile file key
-		l <- calcGitLink dest key
+		l <- inRepo $ gitAnnexLink dest key
 		liftIO $ nukeFile dest
 		addAnnexLink l dest
 		whenM (isDirect) $

Command/Unannex.hs

@@ -60,7 +60,7 @@ cleanup file key = do
   where
 	goFast = do
 		-- fast mode: hard link to content in annex
-		src <- inRepo $ gitAnnexLocation key
+		src <- calcRepo $ gitAnnexLocation key
 		-- creating a hard link could fall; fall back to non fast mode
 		ifM (liftIO $ catchBoolIO $ createLink src file >> return True)
 			( thawContent file

Command/Unlock.hs

@@ -35,7 +35,7 @@ perform dest key = do
 	unlessM (inAnnex key) $ error "content not present"
 	unlessM (checkDiskSpace Nothing key 0) $ error "cannot unlock"
 
-	src <- inRepo $ gitAnnexLocation key
+	src <- calcRepo $ gitAnnexLocation key
 	tmpdest <- fromRepo $ gitAnnexTmpLocation key
 	liftIO $ createDirectoryIfMissing True (parentDir tmpdest)
 	showAction "copying"

Common/Annex.hs

@@ -3,6 +3,6 @@ module Common.Annex (module X) where
 import Common as X
 import Types as X
 import Types.UUID as X (toUUID, fromUUID)
-import Annex as X (gitRepo, inRepo, fromRepo)
+import Annex as X (gitRepo, inRepo, fromRepo, calcRepo)
 import Locations as X
 import Messages as X

Locations.hs

@@ -11,6 +11,7 @@ module Locations (
 	keyPaths,
 	keyPath,
 	gitAnnexLocation,
+	gitAnnexLink,
 	gitAnnexMapping,
 	gitAnnexInodeCache,
 	gitAnnexInodeSentinal,
@@ -88,7 +89,7 @@ annexLocations key = map (annexLocation key) annexHashes
 annexLocation :: Key -> Hasher -> FilePath
 annexLocation key hasher = objectDir </> keyPath key hasher
 
-{- Annexed file's absolute location in a repository.
+{- Annexed object's absolute location in a repository.
  -
  - When there are multiple possible locations, returns the one where the
  - file is actually present.
@@ -99,35 +100,50 @@ annexLocation key hasher = objectDir </> keyPath key hasher
  - This does not take direct mode into account, so in direct mode it is not
  - the actual location of the file's content.
  -}
-gitAnnexLocation :: Key -> Git.Repo -> IO FilePath
+gitAnnexLocation :: Key -> Git.Repo -> GitConfig -> IO FilePath
-gitAnnexLocation key r
+gitAnnexLocation key r config = gitAnnexLocation' key r (annexCrippledFileSystem config)
-	| Git.repoIsLocalBare r =
+gitAnnexLocation' :: Key -> Git.Repo -> Bool -> IO FilePath
-		{- Bare repositories default to hashDirLower for new
+gitAnnexLocation' key r crippled
-		 - content, as it's more portable. -}
+	{- 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
-	| otherwise =
+	{- Non-bare repositories only use hashDirMixed, so
-		{- Non-bare repositories only use hashDirMixed, so
+	 - don't need to do any work to check if the file is
-		 - don't need to do any work to check if the file is
+	 - present. -}
-		 - present. -}
+	| otherwise = return $ inrepo $ annexLocation key hashDirMixed
-		return $ inrepo $ annexLocation key hashDirMixed
   where
 	inrepo d = Git.localGitDir r </> d
 	check locs@(l:_) = fromMaybe l <$> firstM doesFileExist locs
 	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
+	cwd <- getCurrentDirectory
+	let absfile = fromMaybe whoops $ absNormPath cwd file
+	loc <- gitAnnexLocation' key r False
+	return $ relPathDirToFile (parentDir absfile) loc
+  where
+  	whoops = error $ "unable to normalize " ++ file
+
 {- File that maps from a key to the file(s) in the git repository.
  - Used in direct mode. -}
-gitAnnexMapping :: Key -> Git.Repo -> IO FilePath
+gitAnnexMapping :: Key -> Git.Repo -> GitConfig -> IO FilePath
-gitAnnexMapping key r = do
+gitAnnexMapping key r config = do
-	loc <- gitAnnexLocation key r 
+	loc <- gitAnnexLocation key r config
 	return $ loc ++ ".map"
 
 {- File that caches information about a key's content, used to determine
  - if a file has changed.
  - Used in direct mode. -}
-gitAnnexInodeCache :: Key -> Git.Repo -> IO FilePath
+gitAnnexInodeCache :: Key -> Git.Repo -> GitConfig -> IO FilePath
-gitAnnexInodeCache key r  = do
+gitAnnexInodeCache key r config  = do
-	loc <- gitAnnexLocation key r 
+	loc <- gitAnnexLocation key r config
 	return $ loc ++ ".cache"
 
 gitAnnexInodeSentinal :: Git.Repo -> FilePath

Remote/Git.hs

@@ -111,6 +111,7 @@ gen r u _ gc = go <$> remoteCost gc defcst
 				else Nothing
 			, repo = r
 			, gitconfig = gc
+				{ remoteGitConfig = Just $ extractGitConfig r }
 			, readonly = Git.repoIsHttp r
 			, globallyAvailable = not $ Git.repoIsLocal r || Git.repoIsLocalUnknown r
 			, remotetype = remote
@@ -332,7 +333,8 @@ copyFromRemote r key file dest
 copyFromRemoteCheap :: Remote -> Key -> FilePath -> Annex Bool
 copyFromRemoteCheap r key file
 	| not $ Git.repoIsUrl (repo r) = guardUsable (repo r) False $ do
-		loc <- liftIO $ gitAnnexLocation key (repo r)
+		loc <- liftIO $ gitAnnexLocation key (repo r) $
+			fromJust $ remoteGitConfig $ gitconfig r
 		liftIO $ catchBoolIO $ createSymbolicLink loc file >> return True
 	| Git.repoIsSsh (repo r) =
 		ifM (Annex.Content.preseedTmp key file)

Types/GitConfig.hs

@@ -88,7 +88,8 @@ data RemoteGitConfig = RemoteGitConfig
 	, remoteAnnexStartCommand :: Maybe String
 	, remoteAnnexStopCommand :: Maybe String
 
-	-- these settings are specific to particular types of remotes
+	{- These settings are specific to particular types of remotes
+	 - including special remotes. -}
 	, remoteAnnexSshOptions :: [String]
 	, remoteAnnexRsyncOptions :: [String]
 	, remoteAnnexGnupgOptions :: [String]
@@ -97,6 +98,8 @@ data RemoteGitConfig = RemoteGitConfig
 	, remoteAnnexBupSplitOptions :: [String]
 	, remoteAnnexDirectory :: Maybe FilePath
 	, remoteAnnexHookType :: Maybe String
+	{- A regular git remote's git repository config. -}
+	, remoteGitConfig :: Maybe GitConfig
 	}
 
 extractRemoteGitConfig :: Git.Repo -> String -> RemoteGitConfig
@@ -117,6 +120,7 @@ extractRemoteGitConfig r remotename = RemoteGitConfig
 	, remoteAnnexBupSplitOptions = getoptions "bup-split-options"
 	, remoteAnnexDirectory = notempty $ getmaybe "directory"
 	, remoteAnnexHookType = notempty $ getmaybe "hooktype"
+	, remoteGitConfig = Nothing
 	}
   where
 	getbool k def = fromMaybe def $ getmaybebool k

Upgrade/V1.hs

@@ -92,7 +92,7 @@ updateSymlinks = do
 		case r of
 			Nothing -> noop
 			Just (k, _) -> do
-				link <- calcGitLink f k
+				link <- inRepo $ gitAnnexLink f k
 				liftIO $ removeFile f
 				liftIO $ createSymbolicLink link f
 				Annex.Queue.addCommand "add" [Param "--"] [f]

debian/changelog

@@ -30,6 +30,8 @@ git-annex (4.20130324) UNRELEASED; urgency=low
   * webapp: Improved transfer queue management.
   * init: Probe whether the filesystem supports fifos, and if not,
     disable ssh connection caching.
+  * Use lower case hash directories for storing files on crippled filesystems,
+    same as is already done for bare repositories.
 
  -- Joey Hess <joeyh@debian.org>  Mon, 25 Mar 2013 10:21:46 -0400