Clean up comments and restructure read registers

Cleaned up a bunch of comments across the entire code.
Added temporary if routines to check for short circuit on the low side of the h bridge.
Moved most of the read registers, registers to their own functions and made it so that read registers just references the new functions. This was done to facilitate reading only one register while doing a motion command or checking an entire registers condition without having 100+ lines of status printouts to sift through.

testing stall detection in autotune

Added notes in autotune about possible ways to detect stalls and skipped steps in stealth chop and auto tune modes.

errors in tstep capture

Forgot ( ) in the tstep read and save a section of the up motion

autotune routine

Adding autotune routine.
Adding features inside autotune to optimize it and detect stalls

Basic motion Fix

Added a while statement on lines 285 and 287 due to code exiting faster than real-world motion causing the motor to move a small amount and then stop without finishing the move to 100mm and then back to "home".

Submission

Initial release for tracking.