Replace protobuf and remove gogo/protobuf

[boekkooi-terramate]

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Good day!

This PR replaces the direct dependency on github.com/golang/protobuf with google.golang.org/protobuf to avoid using a deprecated package. Doing this included adding the generation code to the Makefile to make it more reproducible.

The PR also removes the gogo/protobuf package as it's deprecated and replaces it with google.golang.org/protobuf. I'm not sure if it makes sense to remove gogo/protobuf but none of the tests started failing so I think it makes sense.

Thanks in advance for reviewing and please let me know if this needs to be split or adjusted.