Make most repository reads policy-aware

Summary: Ref T603. This swaps almost all queries against the repository table over to be policy aware.

Test Plan:
  - Made an audit comment on a commit.
  - Ran `save_lint.php`.
  - Looked up a commit with `diffusion.getcommits`.
  - Looked up lint messages with `diffusion.getlintmessages`.
  - Clicked an external/submodule in Diffusion.
  - Viewed main lint and repository lint in Diffusion.
  - Completed and validated Owners paths in Owners.
  - Executed dry runs via Herald.
  - Queried for package owners with `owners.query`.
  - Viewed Owners package.
  - Edited Owners package.
  - Viewed Owners package list.
  - Executed `repository.query`.
  - Viewed "Repository" tool repository list.
  - Edited Arcanist project.
  - Hit "Delete" on repository (this just tells you to use the CLI).
  - Created a repository.
  - Edited a repository.
  - Ran `bin/repository list`.
  - Ran `bin/search index rGTESTff45d13dffcfb3ea85b03aac8cc36251cacdf01c`
  - Pushed and parsed a commit.
  - Skipped all the Drydock stuff, as it it's hard to test and isn't normally reachable.

Reviewers: btrahan

Reviewed By: btrahan

CC: aran

Maniphest Tasks: T603

Differential Revision: https://secure.phabricator.com/D7132