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Makefile: update protobuf generation instructions #107

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The new instructions work with the latest protoc compiler, which
we can't use inside a Docker container anymore because the Docker
container is three years old and hasn't been updated since. The good
news is the compilation options have gotten much simpler, we don't
need to move files into place anymore.

The new instructions work with the latest protoc compiler, which
we can't use inside a Docker container anymore because the Docker
container is three years old and hasn't been updated since. The good
news is the compilation options have gotten much simpler, we don't
need to move files into place anymore.
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