In "arc patch", update submodules slightly later

Summary:
Ref T13151. See PHI648. With arc patch --nobranch, we update submodules a little too early.

I believe it is safe to just update them a little later, after the intermediate branch management logic runs.

Test Plan: Ran arc patch --nobranch, saw submodule update run later. Not 100% sure this doesn't cause weird issues, but I can't anticipate any.

Reviewers: amckinley, jmeador

Reviewed By: jmeador

Maniphest Tasks: T13151

Differential Revision: https://secure.phabricator.com/D19475