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!

settings.h

@@ -30,7 +30,7 @@
 
 // Version of the EEPROM data. Will be used to migrate existing data from older versions of Grbl
 // when firmware is upgraded. Always stored in byte 0 of eeprom
-#define SETTINGS_VERSION 56
+#define SETTINGS_VERSION 57
 
 // Define bit flag masks for the boolean settings in settings.flag.
 #define BITFLAG_REPORT_INCHES      bit(0)
@@ -39,6 +39,7 @@
 #define BITFLAG_HARD_LIMIT_ENABLE  bit(3)
 #define BITFLAG_HOMING_ENABLE      bit(4)
 #define BITFLAG_SOFT_LIMIT_ENABLE  bit(5)
+#define BITFLAG_INVERT_LIMIT_PINS  bit(6)
 
 // Define EEPROM memory address location values for Grbl settings and parameters
 // NOTE: The Atmega328p has 1KB EEPROM. The upper half is reserved for parameters and
@@ -64,7 +65,8 @@ typedef struct {
   float max_travel[N_AXIS];
   uint8_t pulse_microseconds;
   float default_feed_rate;
-  uint8_t invert_mask;
+  uint8_t step_invert_mask;
+  uint8_t dir_invert_mask;
   uint8_t stepper_idle_lock_time; // If max value 255, steppers do not disable.
   float junction_deviation;
   float arc_tolerance;