Summary:
Running prototool once per proto file causes a variety of problems,
a common one of which is the fact that it will warn on new proto files.

This causes us to lose information about what file the breaking change comes
from but should ease some of the other painpoints from this linter.

Test Plan: Ran `arc lint` after making some breaking proto changes.

Reviewers: michelle, zasgar

Reviewed By: michelle

Differential Revision: https://phab.corp.pixielabs.ai/D9042

GitOrigin-RevId: 72a08085270b7dff3da4dc96384d389be747c82e