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/Init.hs

@@ -113,7 +113,7 @@ initialize' mversion = checkCanInitialize  $ do
 			)
 	whenM versionSupportsUnlockedPointers $ do
 		configureSmudgeFilter
-		scanUnlockedFiles
+		scanUnlockedFiles True
 		unlessM isBareRepo $ do
 			hookWrite postCheckoutHook
 			hookWrite postMergeHook