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/Merge.hs

@@ -26,4 +26,6 @@ start = do
 perform :: CommandPerform
 perform = do
 	Annex.Branch.update
+	-- commit explicitly, in case no remote branches were merged
+	Annex.Branch.commit "update"
 	next $ return True