use queue when upgrading, flushing every so often

Added a cheap way to query the size of a queue.

runQueueAt is not the default yet only because there may be some code that
expects to be able to queue some suff, do something else, and run the whole
queue at the end.

10240 is an arbitrary size for the queue. If we assume annexed
filenames are between 10 and 255 characters long, then the queue will
build up between 100kb and 2550kb long commands. The max command line
length on linux is somewhere above 20k, so this is a fairly good balance --
the queue will buffer only a few megabytes of stuff and a minimal number
of commands will be run by xargs.

Also, insert queue items strictly, this should save memory.

Annex.hs

@@ -16,6 +16,7 @@ module Annex (
 	gitRepo,
 	queue,
 	queueRun,
+	queueRunAt,
 	setConfig,
 	repoConfig
 ) where
@@ -109,6 +110,13 @@ queueRun = do
 	liftIO $ GitQueue.run g q
 	put state { repoqueue = GitQueue.empty }
 
+{- Runs the queue if the specified number of items have been queued. -}
+queueRunAt :: Integer -> Annex ()
+queueRunAt n = do
+	state <- get
+	let q = repoqueue state
+	when (GitQueue.size q >= n) queueRun
+
 {- Changes a git config setting in both internal state and .git/config -}
 setConfig :: String -> String -> Annex ()
 setConfig k value = do

CmdLine.hs

@@ -99,7 +99,7 @@ startup = do
 shutdown :: Annex Bool
 shutdown = do
 	q <- Annex.getState Annex.repoqueue
-	unless (q == GitQueue.empty) $ do
+	unless (0 == GitQueue.size q) $ do
 		showSideAction "Recording state in git..."
 		Annex.queueRun
 

GitQueue.hs

@@ -9,6 +9,7 @@ module GitQueue (
 	Queue,
 	empty,
 	add,
+	size,
 	run
 ) where
 
@@ -31,22 +32,28 @@ data Action = Action {
 {- A queue of actions to perform (in any order) on a git repository,
  - with lists of files to perform them on. This allows coalescing 
  - similar git commands. -}
-type Queue = M.Map Action [FilePath]
+data Queue = Queue Integer (M.Map Action [FilePath])
+	deriving (Show, Eq)
 
 {- Constructor for empty queue. -}
 empty :: Queue
-empty = M.empty
+empty = Queue 0 M.empty
 
 {- Adds an action to a queue. -}
 add :: Queue -> String -> [CommandParam] -> FilePath -> Queue
-add queue subcommand params file = M.insertWith (++) action [file] queue
+add (Queue n m) subcommand params file = Queue (n + 1) m'
 	where
 		action = Action subcommand params
+		m' = M.insertWith' (++) action [file] m
+
+{- Number of items in a queue. -}
+size :: Queue -> Integer
+size (Queue n _) = n
 
 {- Runs a queue on a git repository. -}
 run :: Git.Repo -> Queue -> IO ()
-run repo queue = do
+run repo (Queue _ m) = do
-	forM_ (M.toList queue) $ uncurry $ runAction repo
+	forM_ (M.toList m) $ uncurry $ runAction repo
 	return ()
 
 {- Runs an Action on a list of files in a git repository.

Upgrade/V1.hs

@@ -66,9 +66,10 @@ upgrade = do
 			updateSymlinks
 			moveLocationLogs
 	
+			Annex.queueRun
+
 			-- add new line to auto-merge hashed location logs
 			-- this commits, so has to come after the upgrade
-			g <- Annex.gitRepo
 			liftIO $ Command.Init.gitAttributesWrite g
 
 	setVersion
@@ -92,18 +93,18 @@ updateSymlinks :: Annex ()
 updateSymlinks = do
 	g <- Annex.gitRepo
 	files <- liftIO $ Git.inRepo g [Git.workTree g]
-	forM_ files $ (fixlink g)
+	forM_ files $ fixlink
 	where
-		fixlink g f = do
+		fixlink f = do
 			r <- lookupFile1 f
 			case r of
 				Nothing -> return ()
 				Just (k, _) -> do
 					link <- calcGitLink f k
-					liftIO $ do
+					liftIO $ removeFile f
-						removeFile f
+					liftIO $ createSymbolicLink link f
-						createSymbolicLink link f
+					Annex.queue "add" [Param "--"] f
-						Git.run g "add" [Param "--", File f]
+					Annex.queueRunAt 1024
 
 moveLocationLogs :: Annex ()
 moveLocationLogs = do
@@ -127,11 +128,11 @@ moveLocationLogs = do
 				-- logs that have been pulled from elsewhere
 				old <- liftIO $ readLog f
 				new <- liftIO $ readLog dest
-				liftIO $ do
+				liftIO $ writeLog dest (old++new)
-					writeLog dest (old++new)
+				Annex.queue "add" [Param "--"] dest
-					Git.run g "add" [Param "--", File dest]
+				Annex.queue "add" [Param "--"] f
-					Git.run g "add" [Param "--", File f]
+				Annex.queue "rm" [Param "--quiet", Param "-f", Param "--"] f
-					Git.run g "rm" [Param "--quiet", Param "-f", Param "--", File f]
+				Annex.queueRunAt 1024
 		
 oldlog2key :: FilePath -> Maybe (FilePath, Key)
 oldlog2key l =