Use --user and --password from bin/storage in PHP migrations

Summary:
Fixes T2059. Ref T2517.

Currently, you can run bin/storage upgrade with --user and --password arguments. However, these clownishly apply only to .sql patches -- the .php migrations still use the default user and password.

This is dumb. Stop doing it. Respect --user and --password for PHP patches.

(I implemented "override", which is very similar to "repair", but kept them separate since I think they're semantically distinct enough to differentiate.)

Test Plan: Ran ./bin/storage upgrade --user x --pass y --apply phabricator:20130219.commitsummarymig.php. Verified the correct user and password were used both for the initial connect and patch application.

Reviewers: chad, vrana

Reviewed By: chad

CC: aran

Maniphest Tasks: T2059, T2517

Differential Revision: https://secure.phabricator.com/D5115