Incomplete push but working. Lots more stuff. More to come.

- NEW! An active multi-axis step smoothing algorithm that automatically
adjusts dependent on step frequency. This solves the long standing
issue to aliasing when moving with multiple axes. Similar in scheme to
Smoothieware, but more advanced in ensuring a more consistent CPU
overhead throughout all frequencies while maintaining step exactness.

- Switched from Timer2 to Timer0 for the Step Port Reset Interrupt.
Mainly to free up hardware PWM pins.

- Seperated the direction and step pin assignments, so we can now move
them to seperate ports. This means that we can more easily support 4+
axes in the future.

- Added a setting for inverting the limit pins, as so many users have
request. Better late than never.

- Bug fix related to EEPROM calls when in cycle. The EEPROM would kill
the stepper motion. Now protocol mandates that the system be either in
IDLE or ALARM to access or change any settings.

- Bug fix related to resuming the cycle after a spindle or dwell
command if auto start has been disabled. This fix is somewhat temporary
or more of a patch. Doesn’t work with a straight call-response
streaming protocol, but works fine with serial buffer pre-filling
streaming that most clients use.

- Renamed the pin_map.h to cpu_map.h to more accurately describe what
the file is.

- Pushed an auto start bug fix upon re-initialization.

- Much more polishing to do!
Minor bug fixes: Homing travel calculations. Cycle resuming after spindle and dwell commands.

- Homing travel calculations fixed. It was computing the min travel
rather than max.

- Auto-start disable and pausing after spindle or dwell commands.
Related to plan_synchronize() function call. Now fixed, but still need
to work on the system state.

- Pushed a fix to make this branch more Arduino IDE compatible. Removed
extern call in nuts_bolts.c

- Updated the stepper configuration option of enabling or disabling the
new Adaptive Multi-Axis Step Smoothing Algorithm. Now works either way.

- Updated some copyright info.