Extract core state machine to lua module

[charliefoxtwo]

Extracted a lot of the bios loop into BIOSStateMachine.lua as part of my warpath to remove all dofile calls.

This removes a lot of static calls from Protocol and refactors ProtocolIO to be an instance-based connection manager. The remainder of Protocol likely have to wait until all modules are migrated.

I'm still testing to validate performance is equivalent and that everything works as expected (initial testing would indicate so, but I'd like to continue testing to be on the safe side).

EDIT: In my testing, performance was effectively identical. For my tests, I incremented a counter every time we skipped sending data because we hadn't yet reached the next frame time (1/30 seconds). This happens if we're too quick, so it's generally a good thing. In my testing (on my machine), I found that both my version and the original skipped sending data 3 times between each actual send around 95% of the time. Given the behavior between each version was identical, I'm comfortable moving forward.

[jdahlblom]

5/5 stars, understandable and clean.