commit git-annex branch when copying to a remote (locally)

Otherwise, the location log changes are only staged in its index,
and this can confuse matters if pulling or cloning from the remote.

The test suite was failing because this wasn't done.

CmdLine.hs

@@ -19,7 +19,7 @@ import Control.Monad (when)
 import qualified Annex
 import qualified AnnexQueue
 import qualified GitRepo as Git
-import qualified Branch
+import Content
 import Types
 import Command
 import BackendList
@@ -103,9 +103,6 @@ startup = do
 {- Cleanup actions. -}
 shutdown :: Annex Bool
 shutdown = do
-	AnnexQueue.flush False
-	Branch.commit "update"
-
+	saveState
 	liftIO $ Git.reap
-	
 	return True