Fix a case where upgrade to v7 caused git to think that unlocked files were modified

When a file was already unlocked, but the annex object was present, the
upgrade process populated the unlocked file, but neglected to update the
index.

This commit was sponsored by Jochen Bartl on Patreon.

Annex/WorkTree.hs

@@ -14,6 +14,8 @@ import Annex.Version
 import Annex.Content
 import Annex.ReplaceFile
 import Annex.CurrentBranch
+import Annex.InodeSentinal
+import Utility.InodeCache
 import Config
 import Git.FilePath
 import qualified Git.Ref
@@ -84,9 +86,13 @@ scanUnlockedFiles = whenM (isJust <$> inRepo Git.Branch.current) $ do
 		whenM (inAnnex k) $ do
 			f <- fromRepo $ fromTopFilePath tf
 			destmode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus f
-			replaceFile f $ \tmp ->
+			ic <- replaceFile f $ \tmp ->
 				linkFromAnnex k tmp destmode >>= \case
-					LinkAnnexOk -> return ()
-					LinkAnnexNoop -> return ()
-					LinkAnnexFailed -> liftIO $
+					LinkAnnexOk -> 
+						withTSDelta (liftIO . genInodeCache tmp)
+					LinkAnnexNoop -> return Nothing
+					LinkAnnexFailed -> liftIO $ do
 						writePointerFile tmp k destmode
+						return Nothing
+			liftIO $ print ic
+			maybe noop (restagePointerFile (Restage True) f) ic