improve alwayscommit=false mode

Now changes are staged into the branch's index, but not committed,
which avoids growing a large journal. And sync and merge always
explicitly commit, ensuring that even when they do nothing else,
they commit the staged changes.

Added a flag file to indicate that the branch's journal contains
uncommitted changes. (Could use git ls-files, but don't want to run
that every time.)

In the future, this ability to have uncommitted changes staged in the
journal might be used on remotes after a series of oneshot commands.

Command/Sync.hs

@@ -75,6 +75,7 @@ commit = do
 	showStart "commit" ""
 	next $ next $ do
 		showOutput
+		Annex.Branch.commit "update"
 		-- Commit will fail when the tree is clean, so ignore failure.
 		_ <- inRepo $ Git.Command.runBool "commit"
 			[Param "-a", Param "-m", Param "git-annex automatic sync"]