Direct mode .git/annex/objects directories are no longer left writable

Because that allowed writing to symlinks of files that are not present,
which followed the link and put bad content in an object location.

fsck: Fix up .git/annex/object directory permissions.

This commit was sponsored by an anonymous bitcoin donor.

Command/Fsck.hs

@@ -218,9 +218,10 @@ 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 <- calcRepo $ gitAnnexLocation key
+	file <- calcRepo $ gitAnnexLocation key
+	when (present && not direct) $
 		freezeContent file
+	whenM (liftIO $ doesDirectoryExist $ parentDir file) $
 		freezeContentDir file
 
 	{- In direct mode, modified files will show up as not present,

Command/Indirect.hs

@@ -20,9 +20,9 @@ import Config
 import qualified Annex
 import Annex.Direct
 import Annex.Content
+import Annex.Content.Direct
 import Annex.CatFile
 import Annex.Version
-import Annex.Perms
 import Annex.Exception
 import Init
 import qualified Command.Add
@@ -77,7 +77,8 @@ perform = do
 			Just s
 				| isSymbolicLink s -> void $ flip whenAnnexed f $
 					\_ (k, _) -> do
-						cleandirect k
+						removeInodeCache k
+						removeAssociatedFiles k
 						return Nothing
 				| otherwise -> 
 					maybe noop (fromdirect f)
@@ -87,8 +88,8 @@ perform = do
 
 	fromdirect f k = do
 		showStart "indirect" f
-		thawContentDir =<< calcRepo (gitAnnexLocation k)
-		cleandirect k -- clean before content directory gets frozen
+		removeInodeCache k
+		removeAssociatedFiles k
 		whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
 			v <-tryAnnexIO (moveAnnex k f)
 			case v of
@@ -103,10 +104,6 @@ perform = do
 	warnlocked e = do
 		warning $ show e
 		warning "leaving this file as-is; correct this problem and run git annex add on it"
-
-	cleandirect k = do
-		liftIO . nukeFile =<< calcRepo (gitAnnexInodeCache k)
-		liftIO . nukeFile =<< calcRepo (gitAnnexMapping k)
 	
 cleanup :: CommandCleanup
 cleanup = do