communication_settings.json -> settings.json

I don't think there's value in having lots of settings files,
so I'm going to put the statup settings in there as well.
Rejiggered the communication settings.
Added some mock modules.
Applied a patch to merge logger.

This came from user/BigDCross-logger
Cleaned up the logger a little.
Flushed out directive and stabalization modules.
Patch from user/irwinj_microcontroller_serial
Cleaned up a few style conventions.
The path from directive down to physical works.