fix hard links when upgrading from direct mode

When upgrading a direct mode repo to v7 with adjusted unlocked branches,
fix a bug that prevented annex.thin from taking effect for the files in
working tree.

The hard links used to be ok, but commit 8e22114735 accidentially
broke them. It repopulates the worktree file, which is already a hard link,
and when it's creating the new file, the link count is already 2, and so it
doesn't make a hard link then.

Annex/WorkTree.hs

@@ -75,10 +75,11 @@ ifAnnexed file yes no = maybe no yes =<< lookupFile file
  - when initializing/upgrading a v6+ mode repository.
  -
  - Also, the content for the unlocked file may already be present as
- - an annex object. If so, make the unlocked file use that content.
+ - an annex object. If so, make the unlocked file use that content
+ - when replacefiles is True.
  -}
-scanUnlockedFiles :: Annex ()
-scanUnlockedFiles = whenM (inRepo Git.Ref.headExists) $ do
+scanUnlockedFiles :: Bool -> Annex ()
+scanUnlockedFiles replacefiles = whenM (inRepo Git.Ref.headExists) $ do
 	showSideAction "scanning for unlocked files"
 	Database.Keys.runWriter $
 		liftIO . Database.Keys.SQL.dropAllAssociatedFiles
@@ -97,7 +98,7 @@ scanUnlockedFiles = whenM (inRepo Git.Ref.headExists) $ do
 		let tf = Git.LsTree.file i
 		Database.Keys.runWriter $
 			liftIO . Database.Keys.SQL.addAssociatedFileFast (toIKey k) tf
-		whenM (inAnnex k) $ do
+		whenM (pure replacefiles <&&> inAnnex k) $ do
 			f <- fromRepo $ fromTopFilePath tf
 			destmode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus f
 			ic <- replaceFile f $ \tmp ->