Remove PhabricatorRepository::loadAllByPHIDOrCallsign()

Summary: Ref T603. Move to real Query classes.

Test Plan:

• Ran phd debug pull X (where X does not match a repository).
• Ran phd debug pull Y (where Y does match a repository).
• Ran phd debug pull.
• Ran repository pull.
• Ran repository pull X.
• Ran repository pull Y.
• Ran repository discover.
• Ran repository delete.
• Ran grep.

Reviewers: btrahan

Reviewed By: btrahan

CC: aran

Maniphest Tasks: T603

Differential Revision: https://secure.phabricator.com/D7137