Fix race condition when rebuilding proto files.

[cody-littley]

Why are these changes needed?

There was an odd race condition that would cause make protoc to fail if run multiple times in a row. I think it had something to do with asynchronous file system operations. I didn't totally understand the problem, but deleting the protobuf directories when cleaning make the issue go away.

Checks

• I've made sure the lint is passing in this PR.
• I've made sure the tests are passing. Note that there might be a few flaky tests, in that case, please comment that they are not relevant.
• I've checked the new test coverage and the coverage percentage didn't drop.
• Testing Strategy
  • hand tests
  • Unit tests
  • Integration tests
  • This PR is not tested :(