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/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