unused: Bug fix when a new file was added to the annex, and then removed (but not git rmed). git still has the add staged in this case, so the content should not be unused and was wrongly treated as such.

So, we need to look at both the file on disk to see if it's a annex link,
and the file in the index too. lookupFile doesn't look in the index if the file
is not present on disk.

Command/Unused.hs

@@ -26,6 +26,7 @@ import qualified Git.LsFiles as LsFiles
 import qualified Git.DiffTree as DiffTree
 import qualified Remote
 import qualified Annex.Branch
+import Annex.Link
 import Annex.CatFile
 import Types.Key
 import Types.RefSpec
@@ -214,8 +215,12 @@ withKeysReferenced' mdir initial a = do
 		Just dir -> inRepo $ LsFiles.inRepo [dir]
 	go v [] = return v
 	go v (f:fs) = do
-		x <- lookupFile f
-		case x of
+		mk <- getM id
+			[ isAnnexLink f
+			, liftIO (isPointerFile f)
+			, catKeyFile f
+			]
+		case mk of
 			Nothing -> go v fs
 			Just k -> do
 				!v' <- a k f v