Fix the primary node to actually run it's control loop at 100Hz instead of 95.

Also fix a possible timing bug in other main()s.
Clarify clock configuration code.
Remove unused pin mapping.
Tweak some build settings for the controller.

Set to optimize execution efficiency and to turn off generating a makefile.
Add docs for how to run HIL with the real hardware.
Add a simulator of the plant.

Allows for testing the plant model by just running it open-loop on live data.