fsck: Detect and fix consistency errors in direct mode mapping files.

Command/Fsck.hs

@@ -110,6 +110,7 @@ perform key file backend numcopies = check
 	-- order matters
 	[ fixLink key file
 	, verifyLocationLog key file
+	, verifyDirectMapping key file
 	, checkKeySize key
 	, checkBackend backend key
 	, checkKeyNumCopies key file numcopies
@@ -258,6 +259,19 @@ verifyLocationLog' key desc present u bad = do
 		showNote "fixing location log"
 		bad s
 
+{- Ensures the direct mode mapping file is consistent. Each file
+ - it lists for the key should exist, and the specified file should be
+ - included in it.
+ -}
+verifyDirectMapping :: Key -> FilePath -> Annex Bool
+verifyDirectMapping key file = do
+	whenM isDirect $ do
+		fs <- addAssociatedFile key file
+		forM_ fs $ \f -> 
+			unlessM (liftIO $ doesFileExist f) $
+				void $ removeAssociatedFile key f
+	return True
+
 {- The size of the data for a key is checked against the size encoded in
  - the key's metadata, if available.
  -

debian/changelog

@@ -18,6 +18,7 @@ git-annex (3.20130115) UNRELEASED; urgency=low
   * Fix direct mode mapping code to always store direct mode filenames
     relative to the top of the repository, even when operating inside a
     subdirectory.
+  * fsck: Detect and fix consistency errors in direct mode mapping files.
   * Avoid filename encoding errors when writing direct mode mappings.
 
  -- Joey Hess <joeyh@debian.org>  Mon, 14 Jan 2013 18:35:01 -0400