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!

planner.c

@@ -255,6 +255,7 @@ uint8_t plan_check_full_buffer()
 // during a synchronize call, if it should happen. Also, waits for clean cycle end.
 void plan_synchronize()
 {
+  sys.auto_start = true; // Set auto start to resume cycle after synchronize and caller completes.
   while (plan_get_current_block() || (sys.state == STATE_CYCLE)) { 
     protocol_execute_runtime();   // Check and execute run-time commands
     if (sys.abort) { return; } // Check for system abort