[Native] Remove old protos and related files

Summary:
Remove old protobuf files now that
all references have been updated.

https://linear.app/comm/issue/ENG-1231

Depends on D5045 D5044 D5043 D5042 D4998 D5041 D4995 D4994 D4993 D4992

Test Plan: CI gates pass

Reviewers: atul, abosh, varun, max

Reviewed By: atul

Subscribers: ashoat, tomek

Differential Revision: https://phab.comm.dev/D5046