R1:79abe6653e89

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…