Ports Clean Command to Core

It's all in the title, bro. Ports the clean command to Core and updates the Makefile to get everything to compile as we would like. Addresses #49.
Partially addressed in 62cfb78c658e4b9227c591e69981a129aa16c2f8. See iff you like the solution there. I have an in line comment on that commit that explains another possible way to do it...