protobuf: normalize how protobuf files are generated

The relative paths option for protoc generators doesn't work well when
it comes to dependencies. This simplifies the code generation to avoid
using `go generate` and to use one global command for protoc generation.

This is similar to docker/buildx#2713 since the
same problems with code generation occur here too.

Signed-off-by: Jonathan A. Sternberg <[email protected]>

Author: jsternberg