We can add a maven target / profile to generate the protofiles for us.
Add maven compile-protobuf profile
Alternative route as discussed in the mailing lists: make protobuf required for the maven build. Invoke the PB compiler from maven generate source and remove all generated files from the repo.
Relevant discussion: http://search-hadoop.com/m/ZMVQN1KBQse2/v=threaded
dup of HBASE-10020, see book ref