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 }