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