Lot of refactoring for the future. CoreXY support.

- Rudimentary CoreXY kinematics support. Didn’t test, but homing and
feed holds should work. See config.h. Please report successes and
issues as we find bugs.

- G40 (disable cutter comp) is now “supported”. Meaning that Grbl will
no longer issue an error when typically sent in g-code program header.

- Refactored coolant and spindle state setting into separate functions
for future features.

- Configuration option for fixing homing behavior when there are two
limit switches on the same axis sharing an input pin.

- Created a new “grbl.h” that will eventually be used as the main
include file for Grbl. Also will help simply uploading through the
Arduino IDE

- Separated out the alarms execution flags from the realtime (used be
called runtime) execution flag variable. Now reports exactly what
caused the alarm. Expandable for new alarms later on.

- Refactored the homing cycle to support CoreXY.

- Applied @EliteEng updates to Mega2560 support. Some pins were
reconfigured.

- Created a central step to position and vice versa function. Needed
for non-traditional cartesian machines. Should make it easier later.

- Removed the new CPU map for the Uno. No longer going to used. There
will be only one configuration to keep things uniform.

serial.c

@@ -2,7 +2,7 @@
   serial.c - Low level functions for sending and recieving bytes via the serial port
   Part of Grbl v0.9
 
-  Copyright (c) 2012-2014 Sungeun K. Jeon
+  Copyright (c) 2012-2015 Sungeun K. Jeon
 
   Grbl is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
@@ -98,7 +98,7 @@ void serial_write(uint8_t data) {
   // Wait until there is space in the buffer
   while (next_head == serial_tx_buffer_tail) { 
     // TODO: Restructure st_prep_buffer() calls to be executed here during a long print.    
-    if (sys.execute & EXEC_RESET) { return; } // Only check for abort to avoid an endless loop.
+    if (sys.rt_exec_state & EXEC_RESET) { return; } // Only check for abort to avoid an endless loop.
   }
 
   // Store data and advance head
@@ -170,12 +170,12 @@ ISR(SERIAL_RX)
   uint8_t data = UDR0;
   uint8_t next_head;
   
-  // Pick off runtime command characters directly from the serial stream. These characters are
-  // not passed into the buffer, but these set system state flag bits for runtime execution.
+  // Pick off realtime command characters directly from the serial stream. These characters are
+  // not passed into the buffer, but these set system state flag bits for realtime execution.
   switch (data) {
-    case CMD_STATUS_REPORT: bit_true_atomic(sys.execute, EXEC_STATUS_REPORT); break; // Set as true
-    case CMD_CYCLE_START:   bit_true_atomic(sys.execute, EXEC_CYCLE_START); break; // Set as true
-    case CMD_FEED_HOLD:     bit_true_atomic(sys.execute, EXEC_FEED_HOLD); break; // Set as true
+    case CMD_STATUS_REPORT: bit_true_atomic(sys.rt_exec_state, EXEC_STATUS_REPORT); break; // Set as true
+    case CMD_CYCLE_START:   bit_true_atomic(sys.rt_exec_state, EXEC_CYCLE_START); break; // Set as true
+    case CMD_FEED_HOLD:     bit_true_atomic(sys.rt_exec_state, EXEC_FEED_HOLD); break; // Set as true
     case CMD_RESET:         mc_reset(); break; // Call motion control reset routine.
     default: // Write character to buffer    
       next_head = serial_rx_buffer_head + 1;