This is increasingly difficult to maintain, and has very limited
benefit. Modern coprocessors with enough horsepower to run Java
applications can use the Gradle or Bazel build systems instead.
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.
