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workspace: Remove all dependencies on protobuf (RobotLocomotion#12689)
In common/proto, remove deprecated MakeFileInputStreamOrThrow. In vector_gen, remove support for the protobuf input format. In install, remove CMake find module for Protobuf. In workspace, remove libprotobuf. In setup, remove Ubuntu deps on libprotobuf-dev and python3-protobuf. While we're anyway modifying the setup scripts, also remove macOS's binary setup cleanup step of un-installing dreal.
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