Configure GPIO peripheral

[dyldonahue]

Basically, we need to set up the GPIO peripheral to allow all our io read and writes to work. STM generates the gpio object, but we need to utilize it to replace any of our "digital reads" that are commented out. This ticket involves finding any of our gpio reads and writes (should be through that digitalread and digitalwrite functions) and replace them with HAL stm read and writes. This will involve finding the correct pins within the shepherd ioc file (easiest to use stm32cubeMX) and set these up properly

[dyldonahue]

basically done by accident while getting other stuff working, so closing as complete