Clean Up Firmware

[davidlenfesty]

Move common headers into actual common headers, etc.

[rnpnr]

I'd also like to try and separate all code (and headers) from headers. Its quite ugly and makes building the code really annoying (need workarounds like #pragma once or #ifndef HEADER. After I do that I might write a quick style guide for new code. Clean and consistent code makes it easier to modify and easier for new members to get involved.