Fix a couple of partition migration bugs

Summary:
Ref T11044. Few issues here:

• The PhutilProxyException is missing an argument (hit this while in read-only mode).
• The $ref_key is unused.
• When you add a new master to an existing cluster, we can incorrectly apply .php patches which we should not reapply. Instead, mark them as already-applied.

Test Plan:

• Poked this locally, but will initialize secure004 as an empty master to be sure.

Reviewers: chad, avivey

Reviewed By: avivey

Maniphest Tasks: T11044

Differential Revision: https://secure.phabricator.com/D16916