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.c

@@ -80,7 +80,8 @@ void settings_reset(bool reset_all) {
     settings.acceleration[Y_AXIS] = DEFAULT_Y_ACCELERATION;
     settings.acceleration[Z_AXIS] = DEFAULT_Z_ACCELERATION;
     settings.arc_tolerance = DEFAULT_ARC_TOLERANCE;
-    settings.invert_mask = DEFAULT_STEPPING_INVERT_MASK;
+    settings.step_invert_mask = DEFAULT_STEPPING_INVERT_MASK;
+    settings.dir_invert_mask = DEFAULT_DIRECTION_INVERT_MASK;
     settings.junction_deviation = DEFAULT_JUNCTION_DEVIATION;
   }
   // New settings since last version
@@ -88,6 +89,7 @@ void settings_reset(bool reset_all) {
   if (DEFAULT_REPORT_INCHES) { settings.flags |= BITFLAG_REPORT_INCHES; }
   if (DEFAULT_AUTO_START) { settings.flags |= BITFLAG_AUTO_START; }
   if (DEFAULT_INVERT_ST_ENABLE) { settings.flags |= BITFLAG_INVERT_ST_ENABLE; }
+  if (DEFAULT_INVERT_LIMIT_PINS) { settings.flags |= BITFLAG_INVERT_LIMIT_PINS; }
   if (DEFAULT_SOFT_LIMIT_ENABLE) { settings.flags |= BITFLAG_SOFT_LIMIT_ENABLE; }
   if (DEFAULT_HARD_LIMIT_ENABLE) { settings.flags |= BITFLAG_HARD_LIMIT_ENABLE; }
   if (DEFAULT_HOMING_ENABLE) { settings.flags |= BITFLAG_HOMING_ENABLE; }
@@ -176,46 +178,51 @@ uint8_t settings_store_global_setting(int parameter, float value) {
       if (value < 3) { return(STATUS_SETTING_STEP_PULSE_MIN); }
       settings.pulse_microseconds = round(value); break;
     case 13: settings.default_feed_rate = value; break;
-    case 14: settings.invert_mask = trunc(value); break;
-    case 15: settings.stepper_idle_lock_time = round(value); break;
-    case 16: settings.junction_deviation = fabs(value); break;
-    case 17: settings.arc_tolerance = value; break;
-    case 18: settings.decimal_places = round(value); break;
-    case 19:
+    case 14: settings.step_invert_mask = trunc(value); break;
+    case 15: settings.dir_invert_mask = trunc(value); break;
+    case 16: settings.stepper_idle_lock_time = round(value); break;
+    case 17: settings.junction_deviation = fabs(value); break;
+    case 18: settings.arc_tolerance = value; break;
+    case 19: settings.decimal_places = round(value); break;
+    case 20:
       if (value) { settings.flags |= BITFLAG_REPORT_INCHES; }
       else { settings.flags &= ~BITFLAG_REPORT_INCHES; }
       break;
-    case 20: // Reset to ensure change. Immediate re-init may cause problems.
+    case 21: // Reset to ensure change. Immediate re-init may cause problems.
       if (value) { settings.flags |= BITFLAG_AUTO_START; }
       else { settings.flags &= ~BITFLAG_AUTO_START; }
       break;
-    case 21: // Reset to ensure change. Immediate re-init may cause problems.
+    case 22: // Reset to ensure change. Immediate re-init may cause problems.
       if (value) { settings.flags |= BITFLAG_INVERT_ST_ENABLE; }
       else { settings.flags &= ~BITFLAG_INVERT_ST_ENABLE; }
       break;
-    case 22:
+    case 23: // Reset to ensure change. Immediate re-init may cause problems.
+      if (value) { settings.flags |= BITFLAG_INVERT_LIMIT_PINS; }
+      else { settings.flags &= ~BITFLAG_INVERT_LIMIT_PINS; }
+      break;
+    case 24:
       if (value) { 
         if (bit_isfalse(settings.flags, BITFLAG_HOMING_ENABLE)) { return(STATUS_SOFT_LIMIT_ERROR); }
         settings.flags |= BITFLAG_SOFT_LIMIT_ENABLE; 
       } else { settings.flags &= ~BITFLAG_SOFT_LIMIT_ENABLE; }
       break;
-    case 23:
+    case 25:
       if (value) { settings.flags |= BITFLAG_HARD_LIMIT_ENABLE; }
       else { settings.flags &= ~BITFLAG_HARD_LIMIT_ENABLE; }
       limits_init(); // Re-init to immediately change. NOTE: Nice to have but could be problematic later.
       break;
-    case 24:
+    case 26:
       if (value) { settings.flags |= BITFLAG_HOMING_ENABLE; }
       else { 
         settings.flags &= ~BITFLAG_HOMING_ENABLE; 
-        settings.flags &= ~BITFLAG_SOFT_LIMIT_ENABLE; 
+        settings.flags &= ~BITFLAG_SOFT_LIMIT_ENABLE; // Force disable soft-limits.
       }
       break;
-    case 25: settings.homing_dir_mask = trunc(value); break;
-    case 26: settings.homing_feed_rate = value; break;
-    case 27: settings.homing_seek_rate = value; break;
-    case 28: settings.homing_debounce_delay = round(value); break;
-    case 29: settings.homing_pulloff = value; break;
+    case 27: settings.homing_dir_mask = trunc(value); break;
+    case 28: settings.homing_feed_rate = value; break;
+    case 29: settings.homing_seek_rate = value; break;
+    case 30: settings.homing_debounce_delay = round(value); break;
+    case 31: settings.homing_pulloff = value; break;
     default: 
       return(STATUS_INVALID_STATEMENT);
   }