Fix protobuf gem
This is my second attempt at fixing this. My first attempt was very hacky, you can see it in the earlier commits in this branch. But it found the version from gitlab-rails bundler.
This version has the drawback of a hardcoded version in omnibus for google/protobuf but is a bit cleaner.
Closes: https://gitlab.com/gitlab-org/omnibus-gitlab/issues/2042