Lots of re-organization and cleaning-up. Some bug fixes.

- Added a new source and header file called system. These files contain
the system commands and variables, as well as all of the system headers
and standard libraries Grbl uses. Centralizing some of the code.

- Re-organized the include headers throughout the source code.

- ENABLE_M7 define was missing from config.h. Now there.

- SPINDLE_MAX_RPM and SPINDLE_MIN_RPM now defined in config.h. No
uncommenting to prevent user issues. Minimum spindle RPM now provides
the lower, near 0V, scale adjustment, i.e. some spindles can go really
slow so why use up our 256 voltage bins for them?

- Remove some persistent variables from coolant and spindle control.
They were redundant.

- Removed a VARIABLE_SPINDLE define in cpu_map.h that shouldn’t have
been there.

- Changed the DEFAULT_ARC_TOLERANCE to 0.002mm to improve arc tracing.
Before we had issues with performance, no longer.

- Fixed a bug with the hard limits and the software debounce feature
enabled. The invert limit pin setting wasn’t honored.

- Fixed a bug with the homing direction mask. Now is like it used to
be. At least for now.

- Re-organized main.c to serve as only as the reset/initialization
routine. Makes things a little bit clearer in terms of execution
procedures.

- Re-organized protocol.c as the overall master control unit for
execution procedures. Not quite there yet, but starting to make a
little more sense in how things are run.

- Removed updating of old settings records. So many new settings have
been added that it’s not worth adding the code to migrate old user
settings.

- Tweaked spindle_control.c a bit and made it more clear and consistent
with other parts of Grbl.

- Tweaked the stepper disable bit code in stepper.c. Requires less
flash memory.