Proper Cython support

[standage]

Until recently, the setup.py file was intended to dynamically detect whether Cython was installed. If it was, extensions would be built directly from the Cython files. If not, it would default to the Cythonized C/C++ files. It never really worked though, and we started running into dependency issues---we need to parse setup.py to determine the Cython is a dependency, but Cython is referenced in setup.py.

This dependency hell was resolved recently in #1884, and Cython was completely excised from the automated build process. It would be better to implement the desired behavior (as described above) properly. This issue is a placeholder and reminder to do this.