Respect user/pass flags to bin/storage for direct DatabaseRef-based queries

Summary:
Ref T11893. Previously, we excuted all bin/storage queries through StorageManagementAPI objects.

After D16848, we execute some queries through PhabricatorDatabaseRef. However, the refs we use weren't getting passed the -u / -p flags correctly, for specifying alternate administrative credentials.

Test Plan:

• Created a second account (trunk).
• Ran bin/storage -u trunk.
• Made libphutil throw when not connecting as that user.
• Before patch: some connections incorrectly used the default user, "root".
• After patch: all connections correctly used the configured user, "trunk".

Reviewers: chad

Reviewed By: chad

Maniphest Tasks: T11893

Differential Revision: https://secure.phabricator.com/D16901