clean up git-remote-annex git-annex branch handling

Implemented alternateJournal, which git-remote-annex
uses to avoid any writes to the git-annex branch while setting up
a special remote from an annex:: url.

That prevents the remote.log from being overwritten with the special
remote configuration from the url, which might not be 100% the same as
the existing special remote configuration.

And it prevents an overwrite deleting of other stuff that was
already in the remote.log.

Also, when the branch was created by git-remote-annex, only delete it
at the end if nothing else has been written to it by another command.
This fixes the race condition described in
797f27ab05, where git-remote-annex
set up the branch and git-annex init and other commands were
run at the same time and their writes to the branch were lost.

Annex/Branch.hs

@@ -727,7 +727,8 @@ stageJournal :: JournalLocked -> Annex () -> Annex ()
 stageJournal jl commitindex = withIndex $ withOtherTmp $ \tmpdir -> do
 	prepareModifyIndex jl
 	g <- gitRepo
-	let dir = gitAnnexJournalDir g
+	st <- getState
+	let dir = gitAnnexJournalDir st g
 	(jlogf, jlogh) <- openjlog (fromRawFilePath tmpdir)
 	withHashObjectHandle $ \h ->
 		withJournalHandle gitAnnexJournalDir $ \jh ->

Annex/Journal.hs

@@ -7,7 +7,7 @@
  - All files in the journal must be a series of lines separated by
  - newlines.
  -
- - Copyright 2011-2022 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2024 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -23,6 +23,8 @@ import qualified Git
 import Annex.Perms
 import Annex.Tmp
 import Annex.LockFile
+import Annex.BranchState
+import Types.BranchState
 import Utility.Directory.Stream
 import qualified Utility.RawFilePath as R
 
@@ -82,9 +84,10 @@ privateUUIDsKnown' = not . S.null . annexPrivateRepos . Annex.gitconfig
  -}
 setJournalFile :: Journalable content => JournalLocked -> RegardingUUID -> RawFilePath -> content -> Annex ()
 setJournalFile _jl ru file content = withOtherTmp $ \tmp -> do
+	st <- getState
 	jd <- fromRepo =<< ifM (regardingPrivateUUID ru)
-		( return gitAnnexPrivateJournalDir
-		, return gitAnnexJournalDir
+		( return (gitAnnexPrivateJournalDir st)
+		, return (gitAnnexJournalDir st)
 		)
 	-- journal file is written atomically
 	let jfile = journalFile file
@@ -106,9 +109,10 @@ newtype AppendableJournalFile = AppendableJournalFile (RawFilePath, RawFilePath)
  - branch. -}
 checkCanAppendJournalFile :: JournalLocked -> RegardingUUID -> RawFilePath -> Annex (Maybe AppendableJournalFile)
 checkCanAppendJournalFile _jl ru file = do
+	st <- getState
 	jd <- fromRepo =<< ifM (regardingPrivateUUID ru)
-		( return gitAnnexPrivateJournalDir
-		, return gitAnnexJournalDir
+		( return (gitAnnexPrivateJournalDir st)
+		, return (gitAnnexJournalDir st)
 		)
 	let jfile = jd P.</> journalFile file
 	ifM (liftIO $ R.doesPathExist jfile)
@@ -176,14 +180,12 @@ data GetPrivate = GetPrivate Bool
  -}
 getJournalFileStale :: GetPrivate -> RawFilePath -> Annex JournalledContent
 getJournalFileStale (GetPrivate getprivate) file = do
-	-- Optimisation to avoid a second MVar access.
 	st <- Annex.getState id
-	let g = Annex.repo st
 	liftIO $
 		if getprivate && privateUUIDsKnown' st
 		then do
-			x <- getfrom (gitAnnexJournalDir g)
-			getfrom (gitAnnexPrivateJournalDir g) >>= \case
+			x <- getfrom (gitAnnexJournalDir (Annex.branchstate st) (Annex.repo st))
+			getfrom (gitAnnexPrivateJournalDir (Annex.branchstate st) (Annex.repo st)) >>= \case
 				Nothing -> return $ case x of
 					Nothing -> NoJournalledContent
 					Just b -> JournalledContent b
@@ -193,7 +195,7 @@ getJournalFileStale (GetPrivate getprivate) file = do
 					-- happens in a merge of two
 					-- git-annex branches.
 					Just x' -> x' <> y
-		else getfrom (gitAnnexJournalDir g) >>= return . \case
+		else getfrom (gitAnnexJournalDir (Annex.branchstate st) (Annex.repo st)) >>= return . \case
 			Nothing -> NoJournalledContent
 			Just b -> JournalledContent b
   where
@@ -219,18 +221,20 @@ discardIncompleteAppend v
 {- List of existing journal files in a journal directory, but without locking,
  - may miss new ones just being added, or may have false positives if the
  - journal is staged as it is run. -}
-getJournalledFilesStale :: (Git.Repo -> RawFilePath) -> Annex [RawFilePath]
+getJournalledFilesStale :: (BranchState -> Git.Repo -> RawFilePath) -> Annex [RawFilePath]
 getJournalledFilesStale getjournaldir = do
-	g <- gitRepo
-	fs <- liftIO $ catchDefaultIO [] $
-		getDirectoryContents $ fromRawFilePath (getjournaldir g)
+	st <- Annex.getState id
+	let d = getjournaldir (Annex.branchstate st) (Annex.repo st)
+	fs <- liftIO $ catchDefaultIO [] $ 
+		getDirectoryContents (fromRawFilePath d)
 	return $ filter (`notElem` [".", ".."]) $
 		map (fileJournal . toRawFilePath) fs
 
 {- Directory handle open on a journal directory. -}
-withJournalHandle :: (Git.Repo -> RawFilePath) -> (DirectoryHandle -> IO a) -> Annex a
+withJournalHandle :: (BranchState -> Git.Repo -> RawFilePath) -> (DirectoryHandle -> IO a) -> Annex a
 withJournalHandle getjournaldir a = do
-	d <- fromRepo getjournaldir
+	st <- Annex.getState id
+	let d = getjournaldir (Annex.branchstate st) (Annex.repo st)
 	bracket (opendir d) (liftIO . closeDirectory) (liftIO . a)
   where
 	-- avoid overhead of creating the journal directory when it already
@@ -239,9 +243,10 @@ withJournalHandle getjournaldir a = do
 		`catchIO` (const (createAnnexDirectory d >> opendir d))
 
 {- Checks if there are changes in the journal. -}
-journalDirty :: (Git.Repo -> RawFilePath) -> Annex Bool
+journalDirty :: (BranchState -> Git.Repo -> RawFilePath) -> Annex Bool
 journalDirty getjournaldir = do
-	d <- fromRawFilePath <$> fromRepo getjournaldir
+	st <- getState
+	d <- fromRawFilePath <$> fromRepo (getjournaldir st)
 	liftIO $ 
 		(not <$> isDirectoryEmpty d)
 			`catchIO` (const $ doesDirectoryExist d)

Annex/Locations.hs

@@ -118,6 +118,7 @@ import Key
 import Types.UUID
 import Types.GitConfig
 import Types.Difference
+import Types.BranchState
 import qualified Git
 import qualified Git.Types as Git
 import Git.FilePath
@@ -528,15 +529,19 @@ gitAnnexTransferDir r =
 
 {- .git/annex/journal/ is used to journal changes made to the git-annex
  - branch -}
-gitAnnexJournalDir :: Git.Repo -> RawFilePath
-gitAnnexJournalDir r = 
-	P.addTrailingPathSeparator $ gitAnnexDir r P.</> "journal"
+gitAnnexJournalDir :: BranchState -> Git.Repo -> RawFilePath
+gitAnnexJournalDir st r = P.addTrailingPathSeparator $ 
+	case alternateJournal st of
+		Nothing -> gitAnnexDir r P.</> "journal"
+		Just d -> d
 
 {- .git/annex/journal.private/ is used to journal changes regarding private
  - repositories. -}
-gitAnnexPrivateJournalDir :: Git.Repo -> RawFilePath
-gitAnnexPrivateJournalDir r = 
-	P.addTrailingPathSeparator $ gitAnnexDir r P.</> "journal-private"
+gitAnnexPrivateJournalDir :: BranchState -> Git.Repo -> RawFilePath
+gitAnnexPrivateJournalDir st r = P.addTrailingPathSeparator $
+	case alternateJournal st of
+		Nothing -> gitAnnexDir r P.</> "journal-private"
+		Just d -> d
 
 {- Lock file for the journal. -}
 gitAnnexJournalLock :: Git.Repo -> RawFilePath