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!

motion_control.c

@@ -224,12 +224,12 @@ void mc_homing_cycle()
   // Perform homing routine. NOTE: Special motion case. Only system reset works.
   
   // Search to engage all axes limit switches at faster homing seek rate.
-  limits_go_home(HOMING_SEARCH_CYCLE_0, true, false, settings.homing_seek_rate);  // Search cycle 0
+  limits_go_home(HOMING_SEARCH_CYCLE_0, true, settings.homing_seek_rate);  // Search cycle 0
   #ifdef HOMING_SEARCH_CYCLE_1
-    limits_go_home(HOMING_SEARCH_CYCLE_1, true, false, settings.homing_seek_rate);  // Search cycle 1
+    limits_go_home(HOMING_SEARCH_CYCLE_1, true, settings.homing_seek_rate);  // Search cycle 1
   #endif
   #ifdef HOMING_SEARCH_CYCLE_2
-    limits_go_home(HOMING_SEARCH_CYCLE_2, true, false, settings.homing_seek_rate);  // Search cycle 2
+    limits_go_home(HOMING_SEARCH_CYCLE_2, true, settings.homing_seek_rate);  // Search cycle 2
   #endif
     
   // Now in proximity of all limits. Carefully leave and approach switches in multiple cycles
@@ -237,11 +237,11 @@ void mc_homing_cycle()
   int8_t n_cycle = N_HOMING_LOCATE_CYCLE;
   while (n_cycle--) {
     // Leave all switches to release them. After cycles complete, this is machine zero.
-    limits_go_home(HOMING_LOCATE_CYCLE, false, true, settings.homing_feed_rate);
+    limits_go_home(HOMING_LOCATE_CYCLE, false, settings.homing_feed_rate);
 
     if (n_cycle > 0) {
       // Re-approach all switches to re-engage them.
-      limits_go_home(HOMING_LOCATE_CYCLE, true, false, settings.homing_feed_rate);
+      limits_go_home(HOMING_LOCATE_CYCLE, true, settings.homing_feed_rate);
     }
   }
   // -------------------------------------------------------------------------------------
@@ -291,15 +291,23 @@ void mc_homing_cycle()
 }
 
 
-// Auto-cycle start is a user setting that automatically begins the cycle when a user enters
-// a valid motion command either manually or by a streaming tool. This is intended as a beginners
-// feature to help new users to understand g-code. It can be disabled. Otherwise, the normal
-// operation of cycle start is manually issuing a cycle start command whenever the user is
-// ready and there is a valid motion command in the planner queue.
+// Auto-cycle start has two purposes: 1. Resumes a plan_synchronize() call from a function that
+// requires the planner buffer to empty (spindle enable, dwell, etc.) 2. As a user setting that 
+// automatically begins the cycle when a user enters a valid motion command manually. This is 
+// intended as a beginners feature to help new users to understand g-code. It can be disabled
+// as a beginner tool, but (1.) still operates. If disabled, the operation of cycle start is
+// manually issuing a cycle start command whenever the user is ready and there is a valid motion 
+// command in the planner queue.
 // NOTE: This function is called from the main loop and mc_line() only and executes when one of
 // two conditions exist respectively: There are no more blocks sent (i.e. streaming is finished, 
 // single commands), or the planner buffer is full and ready to go.
-void mc_auto_cycle_start() { if (sys.auto_start) { st_cycle_start(); } }
+void mc_auto_cycle_start() 
+{ 
+  if (sys.auto_start) { 
+    st_cycle_start(); 
+    if (bit_isfalse(settings.flags,BITFLAG_AUTO_START)) { sys.auto_start = false; } // Reset auto start per settings.
+  }
+}
 
 
 // Method to ready the system to reset by setting the runtime reset command and killing any