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

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 ->

CHANGELOG

@@ -5,6 +5,9 @@ git-annex (7.20190820) UNRELEASED; urgency=medium
     so error out to avoid confusion.
   * assistant: When creating a new repository, no longer use direct
     mode, instead use v7 adjusted branches with annex.thin.
+  * 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.
 
  -- Joey Hess <id@joeyh.name>  Sat, 24 Aug 2019 12:54:35 -0400
 

Upgrade/V5.hs

@@ -1,6 +1,6 @@
 {- git-annex v5 -> v6 upgrade support
  -
- - Copyright 2015-2016 Joey Hess <id@joeyh.name>
+ - Copyright 2015-2019 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -35,7 +35,25 @@ upgrade :: Bool -> Annex Bool
 upgrade automatic = do
 	unless automatic $
 		showAction "v5 to v6"
-	whenM isDirect $ do
+	ifM isDirect
+		( do
+			convertDirect automatic
+			-- Worktree files are already populated, so don't
+			-- have this try to populate them again.
+			scanUnlockedFiles False
+		, scanUnlockedFiles True
+		)
+	configureSmudgeFilter
+	-- Inode sentinal file was only used in direct mode and when
+	-- locking down files as they were added. In v6, it's used more
+	-- extensively, so make sure it exists, since old repos that didn't
+	-- use direct mode may not have created it.
+	unlessM (isDirect) $
+		createInodeSentinalFile True
+	return True
+
+convertDirect :: Bool -> Annex ()
+convertDirect automatic = do
 	{- Direct mode makes the same tradeoff of using less disk
 	 - space, with less preservation of old versions of files
 	 - as does annex.thin. -}
@@ -63,15 +81,6 @@ upgrade automatic = do
 	 - contents too, don't use git checkout to check out the
 	 - adjust branch. Instead, update HEAD manually. -}
 	inRepo $ setHeadRef b
-	scanUnlockedFiles
-	configureSmudgeFilter
-	-- Inode sentinal file was only used in direct mode and when
-	-- locking down files as they were added. In v6, it's used more
-	-- extensively, so make sure it exists, since old repos that didn't
-	-- use direct mode may not have created it.
-	unlessM (isDirect) $
-		createInodeSentinalFile True
-	return True
 
 upgradeDirectCommit :: Bool -> String -> Annex ()
 upgradeDirectCommit automatic msg =