make startup scan for deleted files work in direct mode

git add --update cannot be used, because it'll stage typechanged direct
mode files. Intead, use ls-files to find deleted files, and stage them
ourselves.

It seems that no commit was made before when the scan staged deleted files.
(Probably masked since if files were added, a commit happened then..)
Now that I'm doing the staging, I was also able to fix that bug.

Assistant/Threads/Watcher.hs

@@ -27,9 +27,10 @@ import Utility.Types.DirWatcher
 import Utility.Lsof
 import qualified Annex
 import qualified Annex.Queue
-import qualified Git.Command
+import qualified Git
 import qualified Git.UpdateIndex
 import qualified Git.HashObject
+import qualified Git.LsFiles as LsFiles
 import qualified Backend
 import Annex.Content
 import Annex.CatFile
@@ -83,9 +84,15 @@ startupScan scanner = do
 
 		-- Notice any files that were deleted before
 		-- watching was started.
-		liftAnnex $ do
-			inRepo $ Git.Command.run "add" [Param "--update"]
-			showAction "started"
+		top <- liftAnnex $ fromRepo Git.repoPath
+		(fs, cleanup) <- liftAnnex $ inRepo $ LsFiles.deleted [top]
+		forM_ fs $ \f -> do
+			liftAnnex $ Annex.Queue.addUpdateIndex =<<
+				inRepo (Git.UpdateIndex.unstageFile f)
+			maybe noop recordChange =<< madeChange f RmChange
+		void $ liftIO $ cleanup
+		
+		liftAnnex $ showAction "started"
 		
 		modifyDaemonStatus_ $ \s -> s { scanComplete = True }
 

Git/LsFiles.hs

@@ -8,6 +8,7 @@
 module Git.LsFiles (
 	inRepo,
 	notInRepo,
+	deleted,
 	staged,
 	stagedNotDeleted,
 	stagedDetails,
@@ -38,6 +39,13 @@ notInRepo include_ignored l repo = pipeNullSplit params repo
 		| include_ignored = []
 		| otherwise = [Param "--exclude-standard"]
 
+{- Returns a list of files in the specified locations that have been
+ - deleted. -}
+deleted :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+deleted l repo = pipeNullSplit params repo
+  where
+	params = [Params "ls-files --deleted -z --"] ++ map File l
+
 {- Returns a list of all files that are staged for commit. -}
 staged :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)
 staged = staged' []
@@ -112,7 +120,7 @@ data Unmerged = Unmerged
  -   1 = old version, can be ignored
  -   2 = us
  -   3 = them
- - If a line is omitted, that side deleted the file.
+ - If a line is omitted, that side removed the file.
  -}
 unmerged :: [FilePath] -> Repo -> IO ([Unmerged], IO Bool)
 unmerged l repo = do
@@ -157,11 +165,11 @@ reduceUnmerged c (i:is) = reduceUnmerged (new:c) rest
 		, unmergedBlobType = Conflicting blobtypeA blobtypeB
 		, unmergedSha = Conflicting shaA shaB
 		}
-	findsib templatei [] = ([], deleted templatei)
+	findsib templatei [] = ([], removed templatei)
 	findsib templatei (l:ls)
 		| ifile l == ifile templatei = (ls, l)
-		| otherwise = (l:ls, deleted templatei)
-	deleted templatei = templatei
+		| otherwise = (l:ls, removed templatei)
+	removed templatei = templatei
 		{ isus = not (isus templatei)
 		, iblobtype = Nothing
 		, isha = Nothing