Fix bad automatic merge conflict resolution between an annexed file and a directory with the same name when in an adjusted branch.

When running in an overlay work tree, all unchanged files show as deleted,
so this code that stages deletions should not run.

Annex/AutoMerge.hs

@@ -121,7 +121,7 @@ resolveMerge us them inoverlay = do
 	let merged = not (null mergedfs')
 	void $ liftIO cleanup
 
-	unlessM isDirect $ do
+	unlessM (pure inoverlay <||> isDirect) $ do
 		(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
 		unless (null deleted) $
 			Annex.Queue.addCommand "rm"

CHANGELOG

@@ -20,6 +20,8 @@ git-annex (6.20160528) UNRELEASED; urgency=medium
   * list: Do not include dead repositories.
   * move --to: Better behavior when system is completely out of disk space;
     drop content from disk before writing location log.
+  * Fix bad automatic merge conflict resolution between an annexed file
+    and a directory with the same name when in an adjusted branch.
 
  -- Joey Hess <id@joeyh.name>  Fri, 27 May 2016 13:12:48 -0400