re-add lock journal before reading journal files

This reverts commit 2e6e9876e3.

This is gonna be needed after all.. The append will only be atomic if
the journal is locked, because the file being appended will have to be
moved out of the way to avoid an old version of git-annex seeing an
incomplete write to it. When git-annex finds that the file is not in the
journal, and checks the append location, locking will be needed to avoid
a race causing it to miss it in the append location too due to it being
moved back to the journal.

Annex/Branch.hs

@@ -236,7 +236,7 @@ updateTo' pairs = do
 			else return $ "merging " ++
 				unwords (map Git.Ref.describe branches) ++ 
 				" into " ++ fromRef name
-		localtransitions <- getLocalTransitions
+		localtransitions <- getLocalTransitions jl
 		unless (null tomerge) $ do
 			showSideAction merge_desc
 			mapM_ checkBranchDifferences refs
@@ -265,7 +265,7 @@ updateTo' pairs = do
 		-- Gather any transitions that are new to either the
 		-- local branch or a remote ref, which will need to be
 		-- applied on the fly.
-		localts <- getLocalTransitions
+		localts <- lockJournal getLocalTransitions
 		remotets <- mapM getRefTransitions refs
 		ts <- if all (localts ==) remotets
 			then return []
@@ -307,13 +307,14 @@ get file = do
 			content <- if journalIgnorable st
 				then getRef fullname file
 				else if null (unmergedRefs st) 
-					then getLocal file
+					then lockJournal $ 
+						\jl -> getLocal jl file
 					else unmergedbranchfallback st
 			setCache file content
 			return content
   where
 	unmergedbranchfallback st = do
-		l <- getLocal file
+		l <- lockJournal $ \jl -> getLocal jl file
 		bs <- forM (unmergedRefs st) $ \ref -> getRef ref file
 		let content = l <> mconcat bs
 		return $ applytransitions (unhandledTransitions st) content
@@ -343,7 +344,7 @@ precache file branchcontent = do
 	st <- getState
 	content <- if journalIgnorable st
 		then pure branchcontent
-		else getJournalFileStale (GetPrivate True) file >>= return . \case
+		else lockJournal $ \jl -> getJournalFile jl (GetPrivate True) file >>= return . \case
 			NoJournalledContent -> branchcontent
 			JournalledContent journalcontent -> journalcontent
 			PossiblyStaleJournalledContent journalcontent ->
@@ -354,13 +355,13 @@ precache file branchcontent = do
  - reflect changes in remotes.
  - (Changing the value this returns, and then merging is always the
  - same as using get, and then changing its value.) -}
-getLocal :: RawFilePath -> Annex L.ByteString
+getLocal :: JournalLocked -> RawFilePath -> Annex L.ByteString
-getLocal = getLocal' (GetPrivate True)
+getLocal jl = getLocal' jl (GetPrivate True)
 
-getLocal' :: GetPrivate -> RawFilePath -> Annex L.ByteString
+getLocal' :: JournalLocked -> GetPrivate -> RawFilePath -> Annex L.ByteString
-getLocal' getprivate file = do
+getLocal' jl getprivate file = do
 	fastDebug "Annex.Branch" ("read " ++ fromRawFilePath file)
-	go =<< getJournalFileStale getprivate file
+	go =<< getJournalFile jl getprivate file
   where
 	go NoJournalledContent = getRef fullname file
 	go (JournalledContent journalcontent) = return journalcontent
@@ -394,12 +395,12 @@ getRef ref file = withIndex $ catFile ref file
  - modifes the current content of the file on the branch.
  -}
 change :: Journalable content => RegardingUUID -> RawFilePath -> (L.ByteString -> content) -> Annex ()
-change ru file f = lockJournal $ \jl -> f <$> getToChange ru file >>= set jl ru file
+change ru file f = lockJournal $ \jl -> f <$> getToChange jl ru file >>= set jl ru file
 
 {- Applies a function which can modify the content of a file, or not. -}
 maybeChange :: Journalable content => RegardingUUID -> RawFilePath -> (L.ByteString -> Maybe content) -> Annex ()
 maybeChange ru file f = lockJournal $ \jl -> do
-	v <- getToChange ru file
+	v <- getToChange jl ru file
 	case f v of
 		Just jv ->
 			let b = journalableByteString jv
@@ -446,8 +447,8 @@ changeOrAppend ru file f = lockJournal $ \jl ->
 					oldc <> journalableByteString toappend
 
 {- Only get private information when the RegardingUUID is itself private. -}
-getToChange :: RegardingUUID -> RawFilePath -> Annex L.ByteString
+getToChange :: JournalLocked -> RegardingUUID -> RawFilePath -> Annex L.ByteString
-getToChange ru f = flip getLocal' f . GetPrivate =<< regardingPrivateUUID ru
+getToChange jl ru f = flip (getLocal' jl) f . GetPrivate =<< regardingPrivateUUID ru
 
 {- Records new content of a file into the journal.
  -
@@ -727,10 +728,10 @@ stageJournal jl commitindex = withIndex $ withOtherTmp $ \tmpdir -> do
 		removeWhenExistsWith (R.removeLink) (toRawFilePath jlogf)
 	openjlog tmpdir = liftIO $ openTmpFileIn tmpdir "jlog"
 
-getLocalTransitions :: Annex Transitions
+getLocalTransitions :: JournalLocked -> Annex Transitions
-getLocalTransitions = 
+getLocalTransitions jl = 
 	parseTransitionsStrictly "local"
-		<$> getLocal transitionsLog
+		<$> getLocal jl transitionsLog
 
 {- This is run after the refs have been merged into the index,
  - but before the result is committed to the branch.
@@ -979,7 +980,7 @@ overBranchFileContents' select go st = do
 	-- Check the journal, in case it did not get committed to the branch
 	checkjournal f branchcontent
 		| journalIgnorable st = return branchcontent
-		| otherwise = getJournalFileStale (GetPrivate True) f >>= return . \case
+		| otherwise = lockJournal $ \jl -> getJournalFile jl (GetPrivate True) f >>= return . \case
 			NoJournalledContent -> branchcontent
 			JournalledContent journalledcontent ->
 				Just journalledcontent
@@ -989,7 +990,7 @@ overBranchFileContents' select go st = do
 	drain buf fs = case getnext fs of
 		Just (v, f, fs') -> do
 			liftIO $ putMVar buf fs'
-			content <- getJournalFileStale (GetPrivate True) f >>= \case
+			content <- lockJournal $ \jl -> getJournalFile jl (GetPrivate True) f >>= \case
 				NoJournalledContent -> return Nothing
 				JournalledContent journalledcontent ->
 					return (Just journalledcontent)