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

src/applications/diffusion/protocol/DiffusionRepositoryClusterEngine.php

@@ -175,7 +175,8 @@ final class DiffusionRepositoryClusterEngine extends Phobject {
         pht(
           'Failed to acquire read lock after waiting %s second(s). You '.
           'may be able to retry later.',
-          new PhutilNumber($lock_wait)));
+          new PhutilNumber($lock_wait)),
+        $ex);
     }
 
     $versions = PhabricatorRepositoryWorkingCopyVersion::loadVersions(