fsck: Fix location of annexed files when run in linked worktrees

This cleans up after the bug that was fixed in commit
6a9e923c74
Object files that were stored in the wrong location are rescued,
and after that any wrong location logs will be fixed by the usual fsck.

Annex.hs

@@ -12,6 +12,7 @@ module Annex (
 	AnnexState(..),
 	AnnexRead(..),
 	new,
+	new',
 	run,
 	eval,
 	makeRunner,
@@ -291,10 +292,13 @@ newAnnexState c r = do
  - Ensures the config is read, if it was not already, and performs
  - any necessary git repo fixups. -}
 new :: Git.Repo -> IO (AnnexState, AnnexRead)
-new r = do
+new = new' fixupRepo
+
+new' :: (Git.Repo -> GitConfig -> IO Git.Repo) -> Git.Repo -> IO (AnnexState, AnnexRead)
+new' f r = do
 	r' <- Git.Config.read r
 	let c = extractGitConfig FromGitConfig r'
-	st <- newAnnexState c =<< fixupRepo r' c
+	st <- newAnnexState c =<< f r' c
 	rd <- newAnnexRead c
 	return (st, rd)
 

CHANGELOG

@@ -6,6 +6,8 @@ git-annex (10.20250631) UNRELEASED; urgency=medium
     symlinks, that caused annexed file content to be stored in the wrong
     location inside the git directory, and also caused pointer files to not
     get populated.
+  * fsck: Fix location of annexed files when run in linked worktrees
+    that have experienced the above bug.
   * Fix symlinks generated to annexed content when in adjusted unlocked
     branch in a linked worktree on a filesystem not supporting symlinks.
 

Command/Fsck.hs

@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2010-2023 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2025 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -15,6 +15,7 @@ import qualified Annex
 import qualified Remote
 import qualified Types.Backend
 import qualified Backend
+import qualified Git
 import Annex.Content
 import Annex.Verify
 #ifndef mingw32_HOST_OS
@@ -24,6 +25,7 @@ import Annex.Content.Presence
 import Annex.Content.Presence.LowLevel
 import Annex.Perms
 import Annex.Link
+import Annex.Fixup
 import Logs.Location
 import Logs.Trust
 import Logs.Activity
@@ -102,6 +104,8 @@ seek o = startConcurrency commandStages $ do
 	from <- maybe (pure Nothing) (Just <$$> getParsed) (fsckFromOption o)
 	u <- maybe getUUID (pure . Remote.uuid) from
 	checkDeadRepo u
+	when (isNothing from) $
+		cleanupLinkedWorkTreeBug
 	i <- prepIncremental u (incrementalOpt o)
 	let seeker = AnnexedFileSeeker
 		{ startAction = const $ start from i
@@ -768,4 +772,38 @@ withFsckDb (ContIncremental h) a = a h
 withFsckDb (StartIncremental h) a = a h
 withFsckDb (NonIncremental mh) a = maybe noop a mh
 withFsckDb (ScheduleIncremental _ _ i) a = withFsckDb i a
-
+ 
+-- A bug caused linked worktrees on filesystems not supporting symlinks
+-- to not use the common annex directory, but one annex directory per
+-- linked worktree. Object files could end up stored in those directories.
+--
+-- When run in a linked worktree with its own annex directory that is not a
+-- symlink, move any object files to the right location, and delete the
+-- annex directory.
+cleanupLinkedWorkTreeBug :: Annex ()
+cleanupLinkedWorkTreeBug = 
+	whenM (Annex.inRepo needsGitLinkFixup) $ do
+		r <- Annex.gitRepo
+		-- mainWorkTreePath is set by fixupUnusualRepos.
+		-- Unsetting it makes a version of the Repo that uses
+		-- the wrong object location.
+		let r' = r { Git.mainWorkTreePath = Nothing }
+		let dir = gitAnnexDir r'
+		whenM (liftIO $ dirnotsymlink dir) $ do
+			showSideAction $ "Cleaning up directory " 
+				<> QuotedPath dir
+				<> " created by buggy version of git-annex"
+			(st, rd) <- liftIO $ Annex.new' (\r'' _c -> pure r'') r'
+			ks <- liftIO $ Annex.eval (st, rd) $
+				listKeys InAnnex
+			forM_ ks $ \k -> void $ tryNonAsync $ do
+				loc <- liftIO $ gitAnnexLocation k r'
+					(Annex.gitconfig st)
+				moveAnnex k loc
+			void $ tryNonAsync $ liftIO $
+				removeDirectoryRecursive dir
+  where
+	dirnotsymlink dir = 
+		tryIO (R.getSymbolicLinkStatus (fromOsPath dir)) >>= \case
+			Right st -> return $ not (isSymbolicLink st)
+			Left _ -> return False

doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__.mdwn

@@ -97,3 +97,5 @@ This is on win11.
 Absolutely! Approaching 15 years of bigger, better, faster, more ;-)
 
 [[!tag projects/INM7]]
+
+> [[fixed|done]] --[[Joey]]

doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__/comment_7_cfb97162cd21818995f9d71a5ce3a0d0._comment

@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 7"""
+ date="2025-07-15T17:07:43Z"
+ content="""
+Running `git-annex fsck` in the affected worktree will clean up from this
+bug.
+"""]]