finish fixing direct mode merge bug involving unstaged local files

Added test cases for both ways this can happen, with a conflict involving a
file, or a directory.

Cleaned up resolveMerge to not touch the work tree in direct mode, which
turned out to be the only way to handle things.. And makes it much nicer.

Still need to run test suite on windows.

Command/Sync.hs

@@ -345,6 +345,12 @@ mergeFrom branch = do
  - It's also possible that one side has foo as an annexed file, and
  - the other as a directory or non-annexed file. The annexed file
  - is renamed to resolve the merge, and the other object is preserved as-is.
+ -
+ - In indirect mode, the merge is resolved in the work tree and files
+ - staged, to clean up from a conflicted merge that was run in the work
+ - tree. In direct mode, the work tree is not touched here; files are 
+ - staged to the index, and written to the gitAnnexMergeDir, and later
+ - mergeDirectCleanup handles updating the work tree.
  -}
 resolveMerge :: Annex Bool
 resolveMerge = do
@@ -354,10 +360,11 @@ resolveMerge = do
 	let merged = not (null mergedfs)
 	void $ liftIO cleanup
 
-	(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
-	unless (null deleted) $
-		Annex.Queue.addCommand "rm" [Params "--quiet -f --"] deleted
-	void $ liftIO cleanup2
+	unlessM isDirect $ do
+		(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
+		unless (null deleted) $
+			Annex.Queue.addCommand "rm" [Params "--quiet -f --"] deleted
+		void $ liftIO cleanup2
 
 	when merged $ do
 		unlessM isDirect $
@@ -379,7 +386,7 @@ resolveMerge' u
 		case (kus, kthem) of
 			-- Both sides of conflict are annexed files
 			(Just keyUs, Just keyThem) -> do
-				removeoldfile keyUs
+				unstageoldfile
 				if keyUs == keyThem
 					then makelink keyUs
 					else do
@@ -388,20 +395,15 @@ resolveMerge' u
 				return $ Just file
 			-- Our side is annexed, other side is not.
 			(Just keyUs, Nothing) -> do
-				ifM isDirect
-					( do
-						removeoldfile keyUs
-						makelink keyUs
-						movefromdirectmerge file
-					, do
-						unstageoldfile
-						makelink keyUs
-					)
+				unstageoldfile
+				whenM isDirect $
+					stagefromdirectmergedir file
+				makelink keyUs
 				return $ Just file
 			-- Our side is not annexed, other side is.
 			(Nothing, Just keyThem) -> do
-				makelink keyThem
 				unstageoldfile
+				makelink keyThem
 				return $ Just file
 			-- Neither side is annexed; cannot resolve.
 			(Nothing, Nothing) -> return Nothing
@@ -413,45 +415,34 @@ resolveMerge' u
 	makelink key = do
 		let dest = variantFile file key
 		l <- inRepo $ gitAnnexLink dest key
-		replaceFile dest $ makeAnnexLink l
-		stageSymlink dest =<< hashSymlink l
-		whenM isDirect $
-			toDirect key dest
-	removeoldfile keyUs = do
 		ifM isDirect
-			( removeDirect keyUs file
-			, liftIO $ nukeFile file
+			( do
+				d <- fromRepo gitAnnexMergeDir
+				replaceFile (d </> dest) $ makeAnnexLink l
+			, replaceFile dest $ makeAnnexLink l
 			)
-		Annex.Queue.addCommand "rm" [Params "--quiet -f --"] [file]
-	unstageoldfile = Annex.Queue.addCommand "rm" [Params "--quiet -f --cached --"] [file]
+		stageSymlink dest =<< hashSymlink l
 	getKey select = case select (LsFiles.unmergedSha u) of
 		Nothing -> return Nothing
 		Just sha -> catKey sha symLinkMode
-	
-	{- Move something out of the direct mode merge directory and into
-	 - the git work tree.
-	 -
-	 - On a filesystem not supporting symlinks, this is complicated
-	 - because a directory may contain annex links, but just
-	 - moving them into the work tree will not let git know they are
-	 - symlinks.
-	 -
-	 - Also, if the content of the file is available, make it available
-	 - in direct mode.
-	 -}
-	movefromdirectmerge item = do
+
+	-- removing the conflicted file from cache clears the conflict
+	unstageoldfile = Annex.Queue.addCommand "rm" [Params "--quiet -f --cached --"] [file]
+
+	{- stage an item from the direct mode merge directory -}
+	stagefromdirectmergedir item = do
 		d <- fromRepo gitAnnexMergeDir
-		liftIO $ rename (d </> item) item
-		mapM_ setuplink =<< liftIO (dirContentsRecursive item)
-	setuplink f = do
-		v <- getAnnexLinkTarget f
-		case v of
-			Nothing -> noop
-			Just target -> do
-				unlessM (coreSymlinks <$> Annex.getGitConfig) $
-					addAnnexLink target f
-				maybe noop (`toDirect` f) 
-					(fileKey (takeFileName target))
+		l <- liftIO $ dirContentsRecursive (d </> item)
+		if null l
+			then go (d </> item)
+			else mapM_ go l
+	  where
+	  	go f = do
+			v <- getAnnexLinkTarget f
+			case v of
+				Just target -> stageSymlink f
+					=<< hashSymlink target
+				Nothing -> noop
 
 {- git-merge moves conflicting files away to files
  - named something like f~HEAD or f~branch, but the