libprotobuf is a very annoying dependency to deal with, and with the switch to nanopb for generated C++ code, libprotobuf is only used for dynamic decode in the GUI apps. libprotobuf has been swapped out with upb, a much smaller C-based library that supports reflection and can therefore do dynamic decode. This means we can remove the libprotobuf dependency and stop dealing with build issues because of it.
-DUSE_SYSTEM_EIGEN now only removes include paths for Eigen instead of
drake as well.
The USE_VCPKG flags were renamed to USE_SYSTEM since they seem general
enough for that to work (the find_package() commands work the same way
on Arch).
The system libuv CMake build now works with Linux libuv as well.
