always check with ls-files before adding new files

Makes it safe to use git annex unlock with the watcher/assistant.
And also to mix use of the watcher/assistant with regular files stored in git.

Long ago, I had avoided doing this check, except during the startup scan,
because it would be slow to run ls-files repeatedly.

But then I added the lsof check, and to make that fast, got it to detect
batch file adds. So let's move the ls-files check to also occur when it'll
have a batch, and can check them all with one call.

This does slow down adding a single file by just a bit, but really only
a little bit. (The lsof check is probably more expensive.) It also
speeds up the startup scan, especially when there are lots of new files
found by the scan.

Also, fixed the sleep for annex.delayadd to not run while the threadstate
lock is held, so it doesn't unnecessarily freeze everything else.

Also, --force no longer makes it skip the lsof check, which was not
documented, and seems never a good idea.

3 files changed, 108 insertions, 125 deletions

diff --git a/Assistant/Threads/Committer.hs b/Assistant/Threads/Committer.hs
index 62058f4f4..ab70e02bb 100644
--- a/Assistant/Threads/Committer.hs
+++ b/Assistant/Threads/Committer.hs
@@ -5,6 +5,8 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE CPP #-}
+
 module Assistant.Threads.Committer where
 
 import Assistant.Common
@@ -16,10 +18,10 @@ import Assistant.Threads.Watcher
 import Assistant.TransferQueue
 import Assistant.DaemonStatus
 import Logs.Transfer
-import qualified Annex
 import qualified Annex.Queue
 import qualified Git.Command
 import qualified Git.HashObject
+import qualified Git.LsFiles
 import qualified Git.Version
 import Git.Types
 import qualified Command.Add
@@ -27,6 +29,7 @@ import Utility.ThreadScheduler
 import qualified Utility.Lsof as Lsof
 import qualified Utility.DirWatcher as DirWatcher
 import Types.KeySource
+import Config
 
 import Data.Time.Clock
 import Data.Tuple.Utils
@@ -38,28 +41,32 @@ thisThread = "Committer"
 
 {- This thread makes git commits at appropriate times. -}
 commitThread :: ThreadState -> ChangeChan -> CommitChan -> TransferQueue -> DaemonStatusHandle -> NamedThread
-commitThread st changechan commitchan transferqueue dstatus = thread $ runEvery (Seconds 1) $ do
-	-- We already waited one second as a simple rate limiter.
-	-- Next, wait until at least one change is available for
-	-- processing.
-	changes <- getChanges changechan
-	-- Now see if now's a good time to commit.
-	time <- getCurrentTime
-	if shouldCommit time changes
-		then do
-			readychanges <- handleAdds st changechan transferqueue dstatus changes
-			if shouldCommit time readychanges
-				then do
-					debug thisThread
-						[ "committing"
-						, show (length readychanges)
-						, "changes"
-						]
-					void $ alertWhile dstatus commitAlert $
-						runThreadState st commitStaged
-					recordCommit commitchan (Commit time)
-				else refill readychanges
-		else refill changes
+commitThread st changechan commitchan transferqueue dstatus = thread $ do
+	delayadd <- runThreadState st $
+		maybe delayaddDefault (Just . Seconds) . readish
+			<$> getConfig (annexConfig "delayadd") "" 
+	runEvery (Seconds 1) $ do
+		-- We already waited one second as a simple rate limiter.
+		-- Next, wait until at least one change is available for
+		-- processing.
+		changes <- getChanges changechan
+		-- Now see if now's a good time to commit.
+		time <- getCurrentTime
+		if shouldCommit time changes
+			then do
+				readychanges <- handleAdds delayadd st changechan transferqueue dstatus changes
+				if shouldCommit time readychanges
+					then do
+						debug thisThread
+							[ "committing"
+							, show (length readychanges)
+							, "changes"
+							]
+						void $ alertWhile dstatus commitAlert $
+							runThreadState st commitStaged
+						recordCommit commitchan (Commit time)
+					else refill readychanges
+			else refill changes
 	where
 		thread = NamedThread thisThread
 		refill [] = noop
@@ -109,13 +116,24 @@ shouldCommit now changes
 		len = length changes
 		thisSecond c = now `diffUTCTime` changeTime c <= 1
 
-{- If there are PendingAddChanges, the files have not yet actually been
- - added to the annex (probably), and that has to be done now, before
- - committing.
+{- OSX needs a short delay after a file is added before locking it down,
+ - as pasting a file seems to try to set file permissions or otherwise
+ - access the file after closing it. -}
+delayaddDefault :: Maybe Seconds
+#ifdef darwin_HOST_OS
+delayaddDefault = Just $ Seconds 1
+#else
+delayaddDefault = Nothing
+#endif
+
+{- If there are PendingAddChanges, or InProcessAddChanges, the files
+ - have not yet actually been added to the annex, and that has to be done
+ - now, before committing.
  -
  - Deferring the adds to this point causes batches to be bundled together,
  - which allows faster checking with lsof that the files are not still open
- - for write by some other process.
+ - for write by some other process, and faster checking with git-ls-files
+ - that the files are not already checked into git.
  -
  - When a file is added, Inotify will notice the new symlink. So this waits
  - for additional Changes to arrive, so that the symlink has hopefully been
@@ -128,10 +146,11 @@ shouldCommit now changes
  - Any pending adds that are not ready yet are put back into the ChangeChan,
  - where they will be retried later.
  -}
-handleAdds :: ThreadState -> ChangeChan -> TransferQueue -> DaemonStatusHandle -> [Change] -> IO [Change]
-handleAdds st changechan transferqueue dstatus cs = returnWhen (null pendingadds) $ do
-	(postponed, toadd) <- partitionEithers <$>
-		safeToAdd st pendingadds
+handleAdds :: Maybe Seconds -> ThreadState -> ChangeChan -> TransferQueue -> DaemonStatusHandle -> [Change] -> IO [Change]
+handleAdds delayadd st changechan transferqueue dstatus cs = returnWhen (null incomplete) $ do
+	let (pending, inprocess) = partition isPendingAddChange incomplete
+	pending' <- findnew pending
+	(postponed, toadd) <- partitionEithers <$> safeToAdd delayadd st pending' inprocess
 
 	unless (null postponed) $
 		refillChanges changechan postponed
@@ -141,18 +160,26 @@ handleAdds st changechan transferqueue dstatus cs = returnWhen (null pendingadds
 		if DirWatcher.eventsCoalesce || null added
 			then return $ added ++ otherchanges
 			else do
-				r <- handleAdds st changechan transferqueue dstatus
+				r <- handleAdds delayadd st changechan transferqueue dstatus
 					=<< getChanges changechan
 				return $ r ++ added ++ otherchanges
 	where
-		(pendingadds, otherchanges) = partition isPendingAddChange cs
+		(incomplete, otherchanges) = partition (\c -> isPendingAddChange c || isInProcessAddChange c) cs
+		
+		findnew [] = return []
+		findnew pending = do
+			newfiles <- runThreadState st $
+				inRepo (Git.LsFiles.notInRepo False $ map changeFile pending)
+			-- note: timestamp info is lost here
+			let ts = changeTime (pending !! 0)
+			return $ map (PendingAddChange ts) newfiles
 
 		returnWhen c a
 			| c = return otherchanges
 			| otherwise = a
 
 		add :: Change -> IO (Maybe Change)
-		add change@(PendingAddChange { keySource = ks }) =
+		add change@(InProcessAddChange { keySource = ks }) =
 			alertWhile' dstatus (addFileAlert $ keyFilename ks) $
 				liftM ret $ catchMaybeIO $
 					sanitycheck ks $ runThreadState st $ do
@@ -190,38 +217,43 @@ handleAdds st changechan transferqueue dstatus cs = returnWhen (null pendingadds
 				then a
 				else return Nothing
 
-{- PendingAddChanges can Either be Right to be added now,
+{- Files can Either be Right to be added now,
  - or are unsafe, and must be Left for later.
  -
  - Check by running lsof on the temp directory, which
  - the KeySources are locked down in.
  -}
-safeToAdd :: ThreadState -> [Change] -> IO [Either Change Change]
-safeToAdd st changes = runThreadState st $
-	ifM (Annex.getState Annex.force)
-		( allRight changes -- force bypasses lsof check
-		, do
-			tmpdir <- fromRepo gitAnnexTmpDir
-			openfiles <- S.fromList . map fst3 . filter openwrite <$>
-				liftIO (Lsof.queryDir tmpdir)
-
-			let checked = map (check openfiles) changes
-
-			{- If new events are received when files are closed,
-			 - there's no need to retry any changes that cannot
-			 - be done now. -}
-			if DirWatcher.closingTracked
-				then do
-					mapM_ canceladd $ lefts checked
-					allRight $ rights checked
-				else return checked
-		)
+safeToAdd :: Maybe Seconds -> ThreadState -> [Change] -> [Change] -> IO [Either Change Change]
+safeToAdd _ _ [] [] = return []
+safeToAdd delayadd st pending inprocess = do
+	maybe noop threadDelaySeconds delayadd
+	runThreadState st $ do
+		keysources <- mapM Command.Add.lockDown (map changeFile pending)
+		let inprocess' = map mkinprocess (zip pending keysources)
+		tmpdir <- fromRepo gitAnnexTmpDir
+		openfiles <- S.fromList . map fst3 . filter openwrite <$>
+			liftIO (Lsof.queryDir tmpdir)
+		let checked = map (check openfiles) $ inprocess ++ inprocess'
+
+		{- If new events are received when files are closed,
+		 - there's no need to retry any changes that cannot
+		 - be done now. -}
+		if DirWatcher.closingTracked
+			then do
+				mapM_ canceladd $ lefts checked
+				allRight $ rights checked
+			else return checked
 	where
-		check openfiles change@(PendingAddChange { keySource = ks })
+		check openfiles change@(InProcessAddChange { keySource = ks })
 			| S.member (contentLocation ks) openfiles = Left change
 		check _ change = Right change
 
-		canceladd (PendingAddChange { keySource = ks }) = do
+		mkinprocess (c, ks) = InProcessAddChange
+			{ changeTime = changeTime c
+			, keySource = ks
+			}
+
+		canceladd (InProcessAddChange { keySource = ks }) = do
 			warning $ keyFilename ks
 				++ " still has writers, not adding"
 			-- remove the hard link
diff --git a/Assistant/Threads/SanityChecker.hs b/Assistant/Threads/SanityChecker.hs
index b99d72802..148ae1435 100644
--- a/Assistant/Threads/SanityChecker.hs
+++ b/Assistant/Threads/SanityChecker.hs
@@ -93,7 +93,7 @@ check st dstatus transferqueue changechan = do
 			runThreadState st $ warning msg
 			void $ addAlert dstatus $ sanityCheckFixAlert msg
 		addsymlink file s = do
-			Watcher.runHandler thisThread Nothing st dstatus
+			Watcher.runHandler thisThread st dstatus
 				transferqueue changechan
 				Watcher.onAddSymlink file s
 			insanity $ "found unstaged symlink: " ++ file
diff --git a/Assistant/Threads/Watcher.hs b/Assistant/Threads/Watcher.hs
index 9c3f4a941..1bf9e8581 100644
--- a/Assistant/Threads/Watcher.hs
+++ b/Assistant/Threads/Watcher.hs
@@ -5,8 +5,6 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Assistant.Threads.Watcher (
 	watchThread,
 	checkCanWatch,
@@ -30,14 +28,10 @@ import qualified Annex.Queue
 import qualified Git.Command
 import qualified Git.UpdateIndex
 import qualified Git.HashObject
-import qualified Git.LsFiles
 import qualified Backend
-import qualified Command.Add
 import Annex.Content
 import Annex.CatFile
 import Git.Types
-import Config
-import Utility.ThreadScheduler
 
 import Data.Bits.Utils
 import qualified Data.ByteString.Lazy as L
@@ -60,32 +54,19 @@ needLsof = error $ unlines
 	, "Be warned: This can corrupt data in the annex, and make fsck complain."
 	]
 
-{- OSX needs a short delay after a file is added before locking it down,
- - as pasting a file seems to try to set file permissions or otherwise
- - access the file after closing it. -}
-delayaddDefault :: Maybe Seconds
-#ifdef darwin_HOST_OS
-delayaddDefault = Just $ Seconds 1
-#else
-delayaddDefault = Nothing
-#endif
-
 watchThread :: ThreadState -> DaemonStatusHandle -> TransferQueue -> ChangeChan -> NamedThread
 watchThread st dstatus transferqueue changechan = NamedThread thisThread $ do
-	delayadd <- runThreadState st $
-		maybe delayaddDefault (Just . Seconds) . readish
-			<$> getConfig (annexConfig "delayadd") "" 
-	void $ watchDir "." ignored (hooks delayadd) startup
+	void $ watchDir "." ignored hooks startup
 	debug thisThread [ "watching", "."]
 	where
 		startup = startupScan st dstatus
-		hook delay a = Just $ runHandler thisThread delay st dstatus transferqueue changechan a
-		hooks delayadd = mkWatchHooks
-			{ addHook = hook delayadd onAdd
-			, delHook = hook Nothing onDel
-			, addSymlinkHook = hook Nothing onAddSymlink
-			, delDirHook = hook Nothing onDelDir
-			, errHook = hook Nothing onErr
+		hook a = Just $ runHandler thisThread st dstatus transferqueue changechan a
+		hooks = mkWatchHooks
+			{ addHook = hook onAdd
+			, delHook = hook onDel
+			, addSymlinkHook = hook onAddSymlink
+			, delDirHook = hook onDelDir
+			, errHook = hook onErr
 			}
 
 {- Initial scartup scan. The action should return once the scan is complete. -}
@@ -113,65 +94,35 @@ ignored = ig . takeFileName
 	ig ".gitattributes" = True
 	ig _ = False
 
-type Handler = ThreadName -> Maybe Seconds -> FilePath -> Maybe FileStatus -> DaemonStatusHandle -> TransferQueue -> Annex (Maybe Change)
+type Handler = ThreadName -> FilePath -> Maybe FileStatus -> DaemonStatusHandle -> TransferQueue -> Annex (Maybe Change)
 
 {- Runs an action handler, inside the Annex monad, and if there was a
  - change, adds it to the ChangeChan.
  -
  - Exceptions are ignored, otherwise a whole watcher thread could be crashed.
  -}
-runHandler :: ThreadName -> Maybe Seconds -> ThreadState -> DaemonStatusHandle -> TransferQueue -> ChangeChan -> Handler -> FilePath -> Maybe FileStatus -> IO ()
-runHandler threadname delay st dstatus transferqueue changechan handler file filestatus = void $ do
+runHandler :: ThreadName -> ThreadState -> DaemonStatusHandle -> TransferQueue -> ChangeChan -> Handler -> FilePath -> Maybe FileStatus -> IO ()
+runHandler threadname st dstatus transferqueue changechan handler file filestatus = void $ do
 	r <- tryIO go
 	case r of
 		Left e -> print e
 		Right Nothing -> noop
 		Right (Just change) -> recordChange changechan change
 	where
-		go = runThreadState st $ handler threadname delay file filestatus dstatus transferqueue
+		go = runThreadState st $ handler threadname file filestatus dstatus transferqueue
 
-{- During initial directory scan, this will be run for any regular files
- - that are already checked into git. We don't want to turn those into
- - symlinks, so do a check. This is rather expensive, but only happens
- - during startup.
- -
- - It's possible for the file to still be open for write by some process.
- - This can happen in a few ways; one is if two processes had the file open
- - and only one has just closed it. We want to avoid adding a file to the
- - annex that is open for write, to avoid anything being able to change it.
- -
- - We could run lsof on the file here to check for other writers.
- - But, that's slow, and even if there is currently a writer, we will want
- - to add the file *eventually*. Instead, the file is locked down as a hard
- - link in a temp directory, with its write bits disabled, for later
- - checking with lsof, and a Change is returned containing a KeySource
- - using that hard link. The committer handles running lsof and finishing
- - the add.
- -}
 onAdd :: Handler
-onAdd threadname delay file filestatus dstatus _
-	| maybe False isRegularFile filestatus =
-		ifM (scanComplete <$> liftIO (getDaemonStatus dstatus))
-			( go
-			, ifM (null <$> inRepo (Git.LsFiles.notInRepo False [file]))
-				( noChange
-				, go
-				)
-			)
+onAdd _ file filestatus _ _
+	| maybe False isRegularFile filestatus = pendingAddChange file
 	| otherwise = noChange
 	where
-		go = do
-			liftIO $ do
-				debug threadname ["file added", file]
-				maybe noop threadDelaySeconds delay
-			pendingAddChange =<< Command.Add.lockDown file
 
 {- A symlink might be an arbitrary symlink, which is just added.
  - Or, if it is a git-annex symlink, ensure it points to the content
  - before adding it.
  -}
 onAddSymlink :: Handler
-onAddSymlink threadname _ file filestatus dstatus transferqueue = go =<< Backend.lookupFile file
+onAddSymlink threadname file filestatus dstatus transferqueue = go =<< Backend.lookupFile file
 	where
 		go (Just (key, _)) = do
 			link <- calcGitLink file key
@@ -232,7 +183,7 @@ onAddSymlink threadname _ file filestatus dstatus transferqueue = go =<< Backend
 			| otherwise = noop
 
 onDel :: Handler
-onDel threadname _ file _ _dstatus _ = do
+onDel threadname file _ _dstatus _ = do
 	liftIO $ debug threadname ["file deleted", file]
 	Annex.Queue.addUpdateIndex =<<
 		inRepo (Git.UpdateIndex.unstageFile file)
@@ -246,7 +197,7 @@ onDel threadname _ file _ _dstatus _ = do
  - command to get the recursive list of files in the directory, so rm is
  - just as good. -}
 onDelDir :: Handler
-onDelDir threadname _ dir _ _dstatus _ = do
+onDelDir threadname dir _ _dstatus _ = do
 	liftIO $ debug threadname ["directory deleted", dir]
 	Annex.Queue.addCommand "rm"
 		[Params "--quiet -r --cached --ignore-unmatch --"] [dir]
@@ -254,7 +205,7 @@ onDelDir threadname _ dir _ _dstatus _ = do
 
 {- Called when there's an error with inotify or kqueue. -}
 onErr :: Handler
-onErr _ _ msg _ dstatus _ = do
+onErr _ msg _ dstatus _ = do
 	warning msg
 	void $ liftIO $ addAlert dstatus $ warningAlert "watcher" msg
 	return Nothing