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.hs

@@ -37,7 +37,7 @@ module Annex (
 import Common
 import qualified Git
 import qualified Git.Config
-import Annex.Direct.Fixup
+import Annex.Fixup
 import Git.CatFile
 import Git.CheckAttr
 import Git.CheckIgnore
@@ -183,12 +183,13 @@ newState c r = AnnexState
 	}
 
 {- Makes an Annex state object for the specified git repo.
- - Ensures the config is read, if it was not already. -}
+ - Ensures the config is read, if it was not already, and performs
+ - any necessary git repo fixups. -}
 new :: Git.Repo -> IO AnnexState
 new r = do
 	r' <- Git.Config.read =<< Git.relPath r
 	let c = extractGitConfig r'
-	newState c <$> if annexDirect c then fixupDirect r' else return r'
+	newState c <$> fixupRepo r' c
 
 {- Performs an action in the Annex monad from a starting state,
  - returning a new state. -}