sync: Automatic merge conflict resolution now stages deleted files.

Command/Sync.hs

@@ -223,11 +223,16 @@ resolveMerge = do
 	top <- fromRepo Git.repoPath
 	(fs, cleanup) <- inRepo (LsFiles.unmerged [top])
 	merged <- all id <$> mapM resolveMerge' fs
+	void $ liftIO cleanup
+
+	(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
+	Annex.Queue.addCommand "rm" [Params "--quiet -f --"] deleted
+	void $ liftIO cleanup2
+	
 	when merged $ do
 		Annex.Queue.flush
 		void $ inRepo $ Git.Command.runBool "commit"
 			[Param "-m", Param "git-annex automatic merge conflict fix"]
-	void $ liftIO cleanup
 	return merged
 
 resolveMerge' :: LsFiles.Unmerged -> Annex Bool

debian/changelog

@@ -13,6 +13,7 @@ git-annex (3.20130115) UNRELEASED; urgency=low
   * bugfix: Union merges involving two or more repositories could sometimes
     result in data from one repository getting lost. This could result
     in the location log data becoming wrong, and fsck being needed to fix it.
+  * sync: Automatic merge conflict resolution now stages deleted files.
   * Depend on git 1.7.7.6 for --no-edit. Closes: #698399
 
  -- Joey Hess <joeyh@debian.org>  Mon, 14 Jan 2013 18:35:01 -0400