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/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