Summary:
The prototool excludes needed updating after files were moved.

Now just exclude the physicalpb, since that one is a private protobuf.
Rest are now public, so enforce them.

Test Plan: None

Reviewers: michelle, yzhao, #engineering

Reviewed By: michelle, #engineering

Differential Revision: https://phab.corp.pixielabs.ai/D5953

GitOrigin-RevId: 9a3f32ab7c35756340cea09a6393b5cf55fc6bbf