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.

main.c

@@ -44,10 +44,10 @@ int main(void)
   settings_init(); // Load grbl settings from EEPROM
   stepper_init();  // Configure stepper pins and interrupt timers
   system_init();   // Configure pinout pins and pin-change interrupt
-  sei();
   
   memset(&sys, 0, sizeof(sys));  // Clear all system variables
   sys.abort = true;   // Set abort to complete initialization
+  sei(); // Enable interrupts
 
   // Check for power-up and set system alarm if homing is enabled to force homing cycle
   // by setting Grbl's alarm state. Alarm locks out all g-code commands, including the
@@ -60,9 +60,14 @@ int main(void)
     if (bit_istrue(settings.flags,BITFLAG_HOMING_ENABLE)) { sys.state = STATE_ALARM; }
   #endif
   
+  // Grbl initialization loop upon power-up or a system abort. For the latter, all processes
+  // will return to this loop to be cleanly re-initialized.
   for(;;) {
+
+    // TODO: Separate configure task that require interrupts to be disabled, especially upon
+    // a system abort and ensuring any active interrupts are cleanly reset.
   
-    // Reset the system primary functionality.
+    // Reset Grbl primary systems.
     serial_reset_read_buffer(); // Clear serial read buffer
     gc_init(); // Set g-code parser to default state
     spindle_init();
@@ -81,9 +86,8 @@ int main(void)
     if (bit_istrue(settings.flags,BITFLAG_AUTO_START)) { sys.auto_start = true; }
     else { sys.auto_start = false; }
           
-    // Start main loop. Processes inputs and executes them.
-    // NOTE: Upon a system abort, the main loop returns and re-initializes the system.      
-    protocol_process(); 
+    // Start Grbl main loop. Processes program inputs and executes them.
+    protocol_main_loop();
     
   }
   return 0;   /* Never reached */