Summary:
when prototool is run, it looks through the entire workspace to find all the proto files so it can compare to the proto files in master.
its possible to run into a timeout issue such as: `walking the directory structure looking for proto files timed out after 3s and having seen 23852 files, are you sure you are operating in the right context?`
they did add a config to change the timeout, which is 3s by default... but it was literally just done a month ago and has not made it into a new release of prototool yet: https://github.com/uber/prototool/issues/516

this diff updates the config to avoid looking for protos in some unnecessary directories... this will hopefully help with the timeout issue

Test Plan: ran prototool

Reviewers: zasgar, oazizi, #engineering

Reviewed By: oazizi, #engineering

Differential Revision: https://phab.corp.pixielabs.ai/D4562

GitOrigin-RevId: 70b482c9e7d07a66029028a448c351223f6f07f1