withAltRepo needs a separate queue of changes

The queue could potentially contain changes from before withAltRepo, and
get flushed inside the call, which would apply the changes to the modified
repo.

Or, changes could be queued in withAltRepo that were intended to affect
the modified repo, but don't get flushed until later.

I don't know of any cases where either happens, but better safe than sorry.

Note that this affect withIndexFile, which is used in git-annex branch
updates. So, it potentially makes things slower. Should not be by much;
the overhead consists only of querying the current queue a couple of times,
and potentially flushing changes queued within withAltRepo earlier, that
could have maybe been bundled with other later changes.

Notice in particular that the existing queue is not flushed when calling
withAltRepo. So eg when git annex add needs to stage files in the index,
it will still bundle them together efficiently.

Annex/GitOverlay.hs

@@ -15,6 +15,7 @@ import Git.Types
 import Git.Index
 import Git.Env
 import qualified Annex
+import qualified Annex.Queue
 
 {- Runs an action using a different git index file. -}
 withIndexFile :: FilePath -> Annex a -> Annex a
@@ -71,8 +72,18 @@ withAltRepo
 withAltRepo modrepo unmodrepo a = do
 	g <- gitRepo
 	g' <- liftIO $ modrepo g
-	r <- tryNonAsync $ do
-		Annex.changeState $ \s -> s { Annex.repo = g' }
+	q <- Annex.Queue.get
+	v <- tryNonAsync $ do
+		Annex.changeState $ \s -> s
+			{ Annex.repo = g'
+			-- Start a separate queue for any changes made
+			-- with the modified repo.
+			, Annex.repoqueue = Nothing
+			}
 		a
-	Annex.changeState $ \s -> s { Annex.repo = unmodrepo g (Annex.repo s) }
-	either E.throw return r
+	void $ tryNonAsync Annex.Queue.flush
+	Annex.changeState $ \s -> s
+		{ Annex.repo = unmodrepo g (Annex.repo s)
+		, Annex.repoqueue = Just q
+		}
+	either E.throw return v

Annex/Queue.hs

@@ -13,6 +13,7 @@ module Annex.Queue (
 	flush,
 	flushWhenFull,
 	size,
+	get,
 	mergeFrom,
 ) where