Refactoring and lots of bug fixes. Updated homing cycle.

WARNING: There are still some bugs to be worked out. Please use caution
if you test this firmware.

- Feed holds work much better, but there are still some failure
conditions that need to be worked out. This is the being worked on
currently and a fix is planned to be pushed next.

- Homing cycle refactoring: Slight adjustment of the homing cycle to
allow for limit pins to be shared by different axes, as long as the
shared limit pins are not homed on the same cycle. Also, removed the
LOCATE_CYCLE portion of the homing cycle configuration. It was
redundant.

- Limit pin sharing: (See above). To clear up one or two limit pins for
other IO, limit pins can now be shared. For example, the Z-limit can be
shared with either X or Y limit pins, because it’s on a separate homing
cycle. Hard limit will still work exactly as before.

- Spindle pin output fixed. The pins weren’t getting initialized
correctly.

- Fixed a cycle issue where streaming was working almost like a single
block mode. This was caused by a problem with the spindle_run() and
coolant_run() commands and issuing an unintended planner buffer sync.

- Refactored the cycle_start, feed_hold, and other runtime routines
into the runtime command module, where they should be handled here
only. These were redundant.

- Moved some function calls around into more appropriate source code
modules.

- Fixed the reporting of spindle state.

gcode.c

@@ -24,8 +24,8 @@
 
 #include "system.h"
 #include "settings.h"
+#include "protocol.h"
 #include "gcode.h"
-#include "planner.h"
 #include "motion_control.h"
 #include "spindle_control.h"
 #include "coolant_control.h"
@@ -86,11 +86,6 @@ static float to_millimeters(float value)
 // coordinates, respectively.
 uint8_t gc_execute_line(char *line) 
 {
-
-  // If in alarm state, don't process. Immediately return with error.
-  // NOTE: Might not be right place for this, but also prevents $N storing during alarm.
-  if (sys.state == STATE_ALARM) { return(STATUS_ALARM_LOCK); }
- 
   uint8_t char_counter = 0;  
   char letter;
   float value;
@@ -262,10 +257,14 @@ uint8_t gc_execute_line(char *line)
     //  ([M6]: Tool change should be executed here.)
 
     // [M3,M4,M5]: Update spindle state
-    spindle_run(gc.spindle_direction, gc.spindle_speed);
+    if (bit_istrue(modal_group_words,bit(MODAL_GROUP_7))) {
+      spindle_run(gc.spindle_direction, gc.spindle_speed); 
+    }
   
     // [*M7,M8,M9]: Update coolant state
-    coolant_run(gc.coolant_mode);
+    if (bit_istrue(modal_group_words,bit(MODAL_GROUP_8))) {
+      coolant_run(gc.coolant_mode);
+    }
   }
   
   // [G54,G55,...,G59]: Coordinate system selection
@@ -458,15 +457,15 @@ uint8_t gc_execute_line(char *line)
   
   // M0,M1,M2,M30: Perform non-running program flow actions. During a program pause, the buffer may 
   // refill and can only be resumed by the cycle start run-time command.
-  if (gc.program_flow) {
-    plan_synchronize(); // Finish all remaining buffered motions. Program paused when complete.
+  if (gc.program_flow) { 
+    protocol_buffer_synchronize(); // Finish all remaining buffered motions. Program paused when complete.
     sys.auto_start = false; // Disable auto cycle start. Forces pause until cycle start issued.
-    
+  
     // If complete, reset to reload defaults (G92.2,G54,G17,G90,G94,M48,G40,M5,M9). Otherwise,
     // re-enable program flow after pause complete, where cycle start will resume the program.
     if (gc.program_flow == PROGRAM_FLOW_COMPLETED) { mc_reset(); }
     else { gc.program_flow = PROGRAM_FLOW_RUNNING; }
-  }    
+  }
   
   return(gc.status_code);
 }