flush queue before cleaning cruft

Else, queued file stages won't have reached the index, and it won't find
everthing.

This evidently fixes a reversion in my work today, although I don't see how
I broke it. It didn't use to flush the queue first, before, and worked
somehow.

Test suite for v5 is back to 100% green now.

Annex/AutoMerge.hs

@@ -111,10 +111,10 @@ resolveMerge us them = do
 		void $ liftIO cleanup2
 
 	when merged $ do
+		Annex.Queue.flush
 		unlessM isDirect $ do
 			unstagedmap <- inodeMap $ inRepo $ LsFiles.notInRepo False [top]
 			cleanConflictCruft mergedks' mergedfs' unstagedmap
-		Annex.Queue.flush
 		showLongNote "Merge conflict was automatically resolved; you may want to examine the result."
 	return merged