work around a bug in git

http://marc.info/?l=git&m=140262402204212&w=2

This git bug manifested on FAT and Windows as the test suite failing in 3
places. All involved merge conflict resolution. It turned out that the
associated file mappings were getting messed up, and that happened because
this git bug lost track of what files were supposed to be symlinks.

This commit was sponsored by Eric Kidd.

Annex/Direct.hs

@@ -1,6 +1,6 @@
 {- git-annex direct mode
  -
- - Copyright 2012, 2013 Joey Hess <joey@kitenet.net>
+ - Copyright 2012-2014 Joey Hess <joey@kitenet.net>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -168,7 +168,7 @@ mergeDirect startbranch oldref branch resolvemerge = do
 		createDirectoryIfMissing True d
 
 	withIndexFile tmpi $ do
-		merged <- inRepo (mergein d)
+		merged <- stageMerge d branch
 		r <- if merged
 			then return True
 			else resolvemerge
@@ -176,8 +176,23 @@ mergeDirect startbranch oldref branch resolvemerge = do
 		mergeDirectCommit merged startbranch branch
 		liftIO $ rename tmpi reali
 		return r
-  where
-	mergein d g = Git.Merge.stageMerge branch $
+
+{- Stage a merge into the index, avoiding changing HEAD or the current
+ - branch. -}
+stageMerge :: FilePath -> Git.Branch -> Annex Bool
+stageMerge d branch = do
+	-- XXX A bug in git makes stageMerge unsafe to use if the git repo
+	-- is configured with core.symlinks=false
+	-- Using mergeNonInteractive is not ideal though, since it will
+	-- update the current branch immediately, before the work tree
+	-- has been updated, which would leave things in an inconsistent
+	-- state if mergeDirectCleanup is interrupted.
+	-- <http://marc.info/?l=git&m=140262402204212&w=2>
+	merger <- ifM (coreSymlinks <$> Annex.getGitConfig)
+		( return Git.Merge.stageMerge
+		, return Git.Merge.mergeNonInteractive
+		) 
+	inRepo $ \g -> merger branch $ 
 		g { location = Local { gitdir = Git.localGitDir g, worktree = Just d } }
 
 {- Commits after a direct mode merge is complete, and after the work