Submodules are now supported by git-annex!

Seems to work, but still experimental until it's been tested more.

When repositories are on filesystems not supporting symlinks, the .git dir
symlink trick cannot be used. Since we're going to be in direct mode
anyway, the .git dir symlink is not strictly needed.

However, I have not fixed the code that creates new annex symlinks to
handle this case -- the committed symlinks will be wrong.

git annex sync happens to currently fail in a submodule using direct mode,
because there's no HEAD ref. That also needs to be dealt with to get
this fully working in crippled filesystems.

Leaving http://github.com/datalad/datalad/issues/44 open until these issues
are dealt with.

Annex/Direct.hs

@@ -406,7 +406,25 @@ setDirect wantdirect = do
 	Annex.changeGitConfig $ \c -> c { annexDirect = wantdirect }
   where
 	val = Git.Config.boolConfig wantdirect
-	setbare = setConfig (ConfigKey Git.Config.coreBare) val
+	coreworktree = ConfigKey "core.worktree"
+	indirectworktree = ConfigKey "core.indirect-worktree"
+	setbare = do
+		-- core.worktree is not compatable with
+		-- core.bare; git does not allow both to be set, so
+		-- unset it when enabling direct mode, caching in
+		-- core.indirect-worktree
+		if wantdirect
+			then moveconfig coreworktree indirectworktree
+			else moveconfig indirectworktree coreworktree
+		setConfig (ConfigKey Git.Config.coreBare) val
+	moveconfig src dest = do
+		v <- getConfigMaybe src
+		case v of
+			Nothing -> noop
+			Just wt -> do
+				unsetConfig src
+				setConfig dest wt
+				reloadConfig
 
 {- Since direct mode sets core.bare=true, incoming pushes could change
  - the currently checked out branch. To avoid this problem, HEAD