From 90ad129ad262bd6e785cf11b8387a1c376cdd11a Mon Sep 17 00:00:00 2001
From: Sonny Jeon <chamnit@users.noreply.github.com>
Date: Sun, 16 Aug 2015 22:43:30 -0600
Subject: [PATCH 1/2] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4d6d6a9..c18c710 100644
--- a/README.md
+++ b/README.md
@@ -22,7 +22,7 @@ Grbl includes full acceleration management with look ahead. That means the contr
 ***
 
 ### Official Supporters of the Grbl CNC Project
-[![Carbide3D](http://carbide3d.com/files/logo_240px.png)](http://carbide3d.com)  [![Inventables](https://dzevsq2emy08i.cloudfront.net/paperclip/press_image_uploads/62/low_res/inventables-logo.png)](http://inventables.com)
+![Official Supporters](https://dl.dropboxusercontent.com/u/2221997/Contributors.png)
 
 ***
 

From d226555810cc95a10971f57f685483d1a81af79f Mon Sep 17 00:00:00 2001
From: Sonny Jeon <chamnit@gmail.com>
Date: Wed, 30 Sep 2015 20:53:35 -0600
Subject: [PATCH 2/2] Minor bug fixes.

- G38.x was not printing correctly in the $G g-code state reports. Now
fixed.

- Potential bug regarding volatile variables inside a struct. It has
never been a problem in v0.9, but ran into this during v1.0
development. Just to be safe, the fixes are applied here.

- Updated pre-built firmwares with these two bug fixes.
---
 README.md                    |  4 ++--
 doc/log/commit_log_v0.9i.txt | 14 ++++++++++++++
 grbl/gcode.c                 |  2 +-
 grbl/grbl.h                  |  2 +-
 grbl/limits.c                | 22 +++++++++++-----------
 grbl/main.c                  |  4 ++--
 grbl/motion_control.c        | 22 +++++++++++-----------
 grbl/probe.c                 |  6 +++---
 grbl/protocol.c              | 28 ++++++++++++++--------------
 grbl/report.c                |  2 +-
 grbl/serial.c                | 10 +++++-----
 grbl/stepper.c               |  4 ++--
 grbl/system.c                | 10 +++++-----
 grbl/system.h                | 12 ++++++------
 14 files changed, 78 insertions(+), 64 deletions(-)

diff --git a/README.md b/README.md
index c18c710..7facb9a 100644
--- a/README.md
+++ b/README.md
@@ -27,8 +27,8 @@ Grbl includes full acceleration management with look ahead. That means the contr
 ***
 
 _**Master Branch:**_
-* [Grbl v0.9j Atmega328p 16mhz 115200baud with generic defaults](http://bit.ly/1I8Ey4S) _(2015-07-17)_
-* [Grbl v0.9j Atmega328p 16mhz 115200baud with ShapeOko2 defaults](http://bit.ly/1OjUSia) _(2015-07-17)_
+* [Grbl v0.9j Atmega328p 16mhz 115200baud with generic defaults](http://bit.ly/1I8Ey4S) _(2015-09-30)_
+* [Grbl v0.9j Atmega328p 16mhz 115200baud with ShapeOko2 defaults](http://bit.ly/1OjUSia) _(2015-09-30)_
   - **IMPORTANT INFO WHEN UPGRADING TO GRBL v0.9 :** 
   - Baudrate is now **115200** (Up from 9600). 
   - Homing cycle updated. Located based on switch trigger, rather than release point.
diff --git a/doc/log/commit_log_v0.9i.txt b/doc/log/commit_log_v0.9i.txt
index 4208a60..a3401c2 100644
--- a/doc/log/commit_log_v0.9i.txt
+++ b/doc/log/commit_log_v0.9i.txt
@@ -1,3 +1,17 @@
+----------------
+Date: 2015-08-16
+Author: Sonny Jeon
+Subject: Update README.md
+
+----------------
+Date: 2015-08-14
+Author: Sonny Jeon
+Subject: Individual control pin invert compile-option.
+
+- Control pins may be individually inverted through a
+CONTROL_INVERT_MASK macro. This mask is define in the cpu_map.h file.
+
+
 ----------------
 Date: 2015-07-17
 Author: Sonny Jeon
diff --git a/grbl/gcode.c b/grbl/gcode.c
index c47808e..a0a8ad1 100644
--- a/grbl/gcode.c
+++ b/grbl/gcode.c
@@ -1037,7 +1037,7 @@ uint8_t gc_execute_line(char *line)
 	protocol_buffer_synchronize(); // Sync and finish all remaining buffered motions before moving on.
 	if (gc_state.modal.program_flow == PROGRAM_FLOW_PAUSED) {
 	  if (sys.state != STATE_CHECK_MODE) {
-		bit_true_atomic(sys.rt_exec_state, EXEC_FEED_HOLD); // Use feed hold for program pause.
+		bit_true_atomic(sys_rt_exec_state, EXEC_FEED_HOLD); // Use feed hold for program pause.
 		protocol_execute_realtime(); // Execute suspend.
 	  }
 	} else { // == PROGRAM_FLOW_COMPLETED
diff --git a/grbl/grbl.h b/grbl/grbl.h
index 0913592..85e94e5 100644
--- a/grbl/grbl.h
+++ b/grbl/grbl.h
@@ -23,7 +23,7 @@
 
 // Grbl versioning system
 #define GRBL_VERSION "0.9j"
-#define GRBL_VERSION_BUILD "20150811"
+#define GRBL_VERSION_BUILD "20150930"
 
 // Define standard libraries used by Grbl.
 #include <avr/io.h>
diff --git a/grbl/limits.c b/grbl/limits.c
index 65869d1..9742a32 100644
--- a/grbl/limits.c
+++ b/grbl/limits.c
@@ -101,16 +101,16 @@ uint8_t limits_get_state()
     // locked out until a homing cycle or a kill lock command. Allows the user to disable the hard
     // limit setting if their limits are constantly triggering after a reset and move their axes.
     if (sys.state != STATE_ALARM) { 
-      if (!(sys.rt_exec_alarm)) {
+      if (!(sys_rt_exec_alarm)) {
         #ifdef HARD_LIMIT_FORCE_STATE_CHECK
           // Check limit pin state. 
           if (limits_get_state()) {
             mc_reset(); // Initiate system kill.
-            bit_true_atomic(sys.rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
+            bit_true_atomic(sys_rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
           }
         #else
           mc_reset(); // Initiate system kill.
-          bit_true_atomic(sys.rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
+          bit_true_atomic(sys_rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
         #endif
       }
     }
@@ -122,11 +122,11 @@ uint8_t limits_get_state()
   {
     WDTCSR &= ~(1<<WDIE); // Disable watchdog timer. 
     if (sys.state != STATE_ALARM) {  // Ignore if already in alarm state. 
-      if (!(sys.rt_exec_alarm)) {
+      if (!(sys_rt_exec_alarm)) {
         // Check limit pin state. 
         if (limits_get_state()) {
           mc_reset(); // Initiate system kill.
-          bit_true_atomic(sys.rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
+          bit_true_atomic(sys_rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate hard limit critical event
         }
       }  
     }
@@ -225,17 +225,17 @@ void limits_go_home(uint8_t cycle_mask)
 	  st_prep_buffer(); // Check and prep segment buffer. NOTE: Should take no longer than 200us.
 
 	  // Exit routines: No time to run protocol_execute_realtime() in this loop.
-	  if (sys.rt_exec_state & (EXEC_SAFETY_DOOR | EXEC_RESET | EXEC_CYCLE_STOP)) {
+	  if (sys_rt_exec_state & (EXEC_SAFETY_DOOR | EXEC_RESET | EXEC_CYCLE_STOP)) {
 	    // Homing failure: Limit switches are still engaged after pull-off motion
-		if ( (sys.rt_exec_state & (EXEC_SAFETY_DOOR | EXEC_RESET)) ||  // Safety door or reset issued
+		if ( (sys_rt_exec_state & (EXEC_SAFETY_DOOR | EXEC_RESET)) ||  // Safety door or reset issued
 		     (!approach && (limits_get_state() & cycle_mask)) ||  // Limit switch still engaged after pull-off motion
-		     ( approach && (sys.rt_exec_state & EXEC_CYCLE_STOP)) ) { // Limit switch not found during approach.
+		     ( approach && (sys_rt_exec_state & EXEC_CYCLE_STOP)) ) { // Limit switch not found during approach.
      	  mc_reset(); // Stop motors, if they are running.
 		  protocol_execute_realtime();
 		  return;
 		} else {
 		  // Pull-off motion complete. Disable CYCLE_STOP from executing.
-          bit_false_atomic(sys.rt_exec_state,EXEC_CYCLE_STOP);
+          bit_false_atomic(sys_rt_exec_state,EXEC_CYCLE_STOP);
 		  break;
 		} 
 	  }
@@ -335,7 +335,7 @@ void limits_soft_check(float *target)
       // workspace volume so just come to a controlled stop so position is not lost. When complete
       // enter alarm mode.
       if (sys.state == STATE_CYCLE) {
-        bit_true_atomic(sys.rt_exec_state, EXEC_FEED_HOLD);
+        bit_true_atomic(sys_rt_exec_state, EXEC_FEED_HOLD);
         do {
           protocol_execute_realtime();
           if (sys.abort) { return; }
@@ -343,7 +343,7 @@ void limits_soft_check(float *target)
       }
     
       mc_reset(); // Issue system reset and ensure spindle and coolant are shutdown.
-      bit_true_atomic(sys.rt_exec_alarm, (EXEC_ALARM_SOFT_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate soft limit critical event
+      bit_true_atomic(sys_rt_exec_alarm, (EXEC_ALARM_SOFT_LIMIT|EXEC_CRITICAL_EVENT)); // Indicate soft limit critical event
       protocol_execute_realtime(); // Execute to enter critical event loop and system abort
       return;
     }
diff --git a/grbl/main.c b/grbl/main.c
index be8b938..250baaf 100644
--- a/grbl/main.c
+++ b/grbl/main.c
@@ -77,8 +77,8 @@ int main(void)
 
     // Reset system variables.
     sys.abort = false;
-    sys.rt_exec_state = 0;
-    sys.rt_exec_alarm = 0;
+    sys_rt_exec_state = 0;
+    sys_rt_exec_alarm = 0;
     sys.suspend = false;
           
     // Start Grbl main loop. Processes program inputs and executes them.
diff --git a/grbl/motion_control.c b/grbl/motion_control.c
index 0785200..1da671c 100644
--- a/grbl/motion_control.c
+++ b/grbl/motion_control.c
@@ -227,7 +227,7 @@ void mc_homing_cycle()
   #ifdef LIMITS_TWO_SWITCHES_ON_AXES  
     if (limits_get_state()) { 
       mc_reset(); // Issue system reset and ensure spindle and coolant are shutdown.
-      bit_true_atomic(sys.rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT));
+      bit_true_atomic(sys_rt_exec_alarm, (EXEC_ALARM_HARD_LIMIT|EXEC_CRITICAL_EVENT));
       return;
     }
   #endif
@@ -283,7 +283,7 @@ void mc_homing_cycle()
   // After syncing, check if probe is already triggered. If so, halt and issue alarm.
   // NOTE: This probe initialization error applies to all probing cycles.
   if ( probe_get_state() ) { // Check probe pin state.
-    bit_true_atomic(sys.rt_exec_alarm, EXEC_ALARM_PROBE_FAIL);
+    bit_true_atomic(sys_rt_exec_alarm, EXEC_ALARM_PROBE_FAIL);
     protocol_execute_realtime();
   }
   if (sys.abort) { return; } // Return if system reset has been issued.
@@ -296,10 +296,10 @@ void mc_homing_cycle()
   #endif
   
   // Activate the probing state monitor in the stepper module.
-  sys.probe_state = PROBE_ACTIVE;
+  sys_probe_state = PROBE_ACTIVE;
 
   // Perform probing cycle. Wait here until probe is triggered or motion completes.
-  bit_true_atomic(sys.rt_exec_state, EXEC_CYCLE_START);
+  bit_true_atomic(sys_rt_exec_state, EXEC_CYCLE_START);
   do {
     protocol_execute_realtime(); 
     if (sys.abort) { return; } // Check for system abort
@@ -308,13 +308,13 @@ void mc_homing_cycle()
   // Probing cycle complete!
   
   // Set state variables and error out, if the probe failed and cycle with error is enabled.
-  if (sys.probe_state == PROBE_ACTIVE) {
+  if (sys_probe_state == PROBE_ACTIVE) {
     if (is_no_error) { memcpy(sys.probe_position, sys.position, sizeof(float)*N_AXIS); }
-    else { bit_true_atomic(sys.rt_exec_alarm, EXEC_ALARM_PROBE_FAIL); }
+    else { bit_true_atomic(sys_rt_exec_alarm, EXEC_ALARM_PROBE_FAIL); }
   } else { 
     sys.probe_succeeded = true; // Indicate to system the probing cycle completed successfully.
   }
-  sys.probe_state = PROBE_OFF; // Ensure probe state monitor is disabled.
+  sys_probe_state = PROBE_OFF; // Ensure probe state monitor is disabled.
   protocol_execute_realtime();   // Check and execute run-time commands
   if (sys.abort) { return; } // Check for system abort
 
@@ -342,8 +342,8 @@ void mc_homing_cycle()
 void mc_reset()
 {
   // Only this function can set the system reset. Helps prevent multiple kill calls.
-  if (bit_isfalse(sys.rt_exec_state, EXEC_RESET)) {
-    bit_true_atomic(sys.rt_exec_state, EXEC_RESET);
+  if (bit_isfalse(sys_rt_exec_state, EXEC_RESET)) {
+    bit_true_atomic(sys_rt_exec_state, EXEC_RESET);
 
     // Kill spindle and coolant.   
     spindle_stop();
@@ -354,8 +354,8 @@ void mc_reset()
     // the steppers enabled by avoiding the go_idle call altogether, unless the motion state is
     // violated, by which, all bets are off.
     if ((sys.state & (STATE_CYCLE | STATE_HOMING)) || (sys.suspend == SUSPEND_ENABLE_HOLD)) {
-      if (sys.state == STATE_HOMING) { bit_true_atomic(sys.rt_exec_alarm, EXEC_ALARM_HOMING_FAIL); }
-      else { bit_true_atomic(sys.rt_exec_alarm, EXEC_ALARM_ABORT_CYCLE); }
+      if (sys.state == STATE_HOMING) { bit_true_atomic(sys_rt_exec_alarm, EXEC_ALARM_HOMING_FAIL); }
+      else { bit_true_atomic(sys_rt_exec_alarm, EXEC_ALARM_ABORT_CYCLE); }
       st_go_idle(); // Force kill steppers. Position has likely been lost.
     }
   }
diff --git a/grbl/probe.c b/grbl/probe.c
index 3bba4df..fc95756 100644
--- a/grbl/probe.c
+++ b/grbl/probe.c
@@ -58,11 +58,11 @@ uint8_t probe_get_state() { return((PROBE_PIN & PROBE_MASK) ^ probe_invert_mask)
 // NOTE: This function must be extremely efficient as to not bog down the stepper ISR.
 void probe_state_monitor()
 {
-  if (sys.probe_state == PROBE_ACTIVE) {
+  if (sys_probe_state == PROBE_ACTIVE) {
     if (probe_get_state()) {
-      sys.probe_state = PROBE_OFF;
+      sys_probe_state = PROBE_OFF;
       memcpy(sys.probe_position, sys.position, sizeof(float)*N_AXIS);
-      bit_true(sys.rt_exec_state, EXEC_MOTION_CANCEL);
+      bit_true(sys_rt_exec_state, EXEC_MOTION_CANCEL);
     }
   }
 }
diff --git a/grbl/protocol.c b/grbl/protocol.c
index 858ffef..d07a43a 100644
--- a/grbl/protocol.c
+++ b/grbl/protocol.c
@@ -79,7 +79,7 @@ void protocol_main_loop()
   } else {
     // All systems go! But first check for safety door.
     if (system_check_safety_door_ajar()) {
-      bit_true(sys.rt_exec_state, EXEC_SAFETY_DOOR);
+      bit_true(sys_rt_exec_state, EXEC_SAFETY_DOOR);
       protocol_execute_realtime(); // Enter safety door mode. Should return as IDLE state.
     } else {
       sys.state = STATE_IDLE; // Set system to ready. Clear all state flags.
@@ -180,7 +180,7 @@ void protocol_main_loop()
 // define more computationally-expensive volatile variables. This also provides a controlled way to 
 // execute certain tasks without having two or more instances of the same task, such as the planner
 // recalculating the buffer upon a feedhold or override.
-// NOTE: The sys.rt_exec_state variable flags are set by any process, step or serial interrupts, pinouts,
+// NOTE: The sys_rt_exec_state variable flags are set by any process, step or serial interrupts, pinouts,
 // limit switches, or the main program.
 void protocol_execute_realtime()
 {
@@ -189,7 +189,7 @@ void protocol_execute_realtime()
   do { // If system is suspended, suspend loop restarts here.
     
   // Check and execute alarms. 
-  rt_exec = sys.rt_exec_alarm; // Copy volatile sys.rt_exec_alarm.
+  rt_exec = sys_rt_exec_alarm; // Copy volatile sys_rt_exec_alarm.
   if (rt_exec) { // Enter only if any bit flag is true
     // System alarm. Everything has shutdown by something that has gone severely wrong. Report
     // the source of the error to the user. If critical, Grbl disables by entering an infinite
@@ -209,7 +209,7 @@ void protocol_execute_realtime()
     // Halt everything upon a critical event flag. Currently hard and soft limits flag this.
     if (rt_exec & EXEC_CRITICAL_EVENT) {
       report_feedback_message(MESSAGE_CRITICAL_EVENT);
-      bit_false_atomic(sys.rt_exec_state,EXEC_RESET); // Disable any existing reset
+      bit_false_atomic(sys_rt_exec_state,EXEC_RESET); // Disable any existing reset
       do { 
         // Nothing. Block EVERYTHING until user issues reset or power cycles. Hard limits
         // typically occur while unattended or not paying attention. Gives the user time
@@ -218,17 +218,17 @@ void protocol_execute_realtime()
         // stream could be still engaged and cause a serious crash if it continues afterwards.
         
         // TODO: Allow status reports during a critical alarm. Still need to think about implications of this.
-//         if (sys.rt_exec_state & EXEC_STATUS_REPORT) { 
+//         if (sys_rt_exec_state & EXEC_STATUS_REPORT) { 
 //           report_realtime_status();
-//           bit_false_atomic(sys.rt_exec_state,EXEC_STATUS_REPORT); 
+//           bit_false_atomic(sys_rt_exec_state,EXEC_STATUS_REPORT); 
 //         }
-      } while (bit_isfalse(sys.rt_exec_state,EXEC_RESET));
+      } while (bit_isfalse(sys_rt_exec_state,EXEC_RESET));
     }
-    bit_false_atomic(sys.rt_exec_alarm,0xFF); // Clear all alarm flags
+    bit_false_atomic(sys_rt_exec_alarm,0xFF); // Clear all alarm flags
   }
   
   // Check amd execute realtime commands
-  rt_exec = sys.rt_exec_state; // Copy volatile sys.rt_exec_state.
+  rt_exec = sys_rt_exec_state; // Copy volatile sys_rt_exec_state.
   if (rt_exec) { // Enter only if any bit flag is true
   
     // Execute system abort. 
@@ -240,7 +240,7 @@ void protocol_execute_realtime()
     // Execute and serial print status
     if (rt_exec & EXEC_STATUS_REPORT) { 
       report_realtime_status();
-      bit_false_atomic(sys.rt_exec_state,EXEC_STATUS_REPORT);
+      bit_false_atomic(sys_rt_exec_state,EXEC_STATUS_REPORT);
     }
   
     // Execute hold states.
@@ -291,7 +291,7 @@ void protocol_execute_realtime()
         }
          
       }
-      bit_false_atomic(sys.rt_exec_state,(EXEC_MOTION_CANCEL | EXEC_FEED_HOLD | EXEC_SAFETY_DOOR));      
+      bit_false_atomic(sys_rt_exec_state,(EXEC_MOTION_CANCEL | EXEC_FEED_HOLD | EXEC_SAFETY_DOOR));      
     }
           
     // Execute a cycle start by starting the stepper interrupt to begin executing the blocks in queue.
@@ -326,7 +326,7 @@ void protocol_execute_realtime()
           sys.suspend = SUSPEND_DISABLE; // Break suspend state.
         }
       }    
-      bit_false_atomic(sys.rt_exec_state,EXEC_CYCLE_START);
+      bit_false_atomic(sys_rt_exec_state,EXEC_CYCLE_START);
     }
     
     // Reinitializes the cycle plan and stepper system after a feed hold for a resume. Called by 
@@ -348,7 +348,7 @@ void protocol_execute_realtime()
         sys.suspend = SUSPEND_DISABLE;
         sys.state = STATE_IDLE;
       }
-      bit_false_atomic(sys.rt_exec_state,EXEC_CYCLE_STOP);
+      bit_false_atomic(sys_rt_exec_state,EXEC_CYCLE_STOP);
     }
     
   }
@@ -398,4 +398,4 @@ void protocol_buffer_synchronize()
 // when one of these conditions exist respectively: There are no more blocks sent (i.e. streaming 
 // is finished, single commands), a command that needs to wait for the motions in the buffer to 
 // execute calls a buffer sync, or the planner buffer is full and ready to go.
-void protocol_auto_cycle_start() { bit_true_atomic(sys.rt_exec_state, EXEC_CYCLE_START); } 
+void protocol_auto_cycle_start() { bit_true_atomic(sys_rt_exec_state, EXEC_CYCLE_START); } 
diff --git a/grbl/report.c b/grbl/report.c
index 86782bc..152fabe 100644
--- a/grbl/report.c
+++ b/grbl/report.c
@@ -331,7 +331,7 @@ void report_gcode_modes()
     case MOTION_MODE_NONE : printPgmString(PSTR("G80")); break;
     default: 
       printPgmString(PSTR("G38."));
-      print_uint8_base10(gc_state.modal.motion - (MOTION_MODE_PROBE_TOWARD+2));
+      print_uint8_base10(gc_state.modal.motion - (MOTION_MODE_PROBE_TOWARD-2));
   }
 
   printPgmString(PSTR(" G"));
diff --git a/grbl/serial.c b/grbl/serial.c
index edfbecf..56f84e0 100644
--- a/grbl/serial.c
+++ b/grbl/serial.c
@@ -89,7 +89,7 @@ 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.rt_exec_state & 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
@@ -164,10 +164,10 @@ ISR(SERIAL_RX)
   // 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.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_SAFETY_DOOR:   bit_true_atomic(sys.rt_exec_state, EXEC_SAFETY_DOOR); 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_SAFETY_DOOR:   bit_true_atomic(sys_rt_exec_state, EXEC_SAFETY_DOOR); 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;
diff --git a/grbl/stepper.c b/grbl/stepper.c
index 614a4c8..ce08599 100644
--- a/grbl/stepper.c
+++ b/grbl/stepper.c
@@ -218,7 +218,7 @@ void st_go_idle()
   
   // Set stepper driver idle state, disabled or enabled, depending on settings and circumstances.
   bool pin_state = false; // Keep enabled.
-  if (((settings.stepper_idle_lock_time != 0xff) || sys.rt_exec_alarm) && sys.state != STATE_HOMING) {
+  if (((settings.stepper_idle_lock_time != 0xff) || sys_rt_exec_alarm) && sys.state != STATE_HOMING) {
     // Force stepper dwell to lock axes for a defined amount of time to ensure the axes come to a complete
     // stop and not drift from residual inertial forces at the end of the last movement.
     delay_ms(settings.stepper_idle_lock_time);
@@ -338,7 +338,7 @@ ISR(TIMER1_COMPA_vect)
     } else {
       // Segment buffer empty. Shutdown.
       st_go_idle();
-      bit_true_atomic(sys.rt_exec_state,EXEC_CYCLE_STOP); // Flag main program for cycle end
+      bit_true_atomic(sys_rt_exec_state,EXEC_CYCLE_STOP); // Flag main program for cycle end
       return; // Nothing to do but exit.
     }  
   }
diff --git a/grbl/system.c b/grbl/system.c
index 1a11d3e..b3371d9 100644
--- a/grbl/system.c
+++ b/grbl/system.c
@@ -49,13 +49,13 @@ ISR(CONTROL_INT_vect)
     if (bit_istrue(pin,bit(RESET_BIT))) {
       mc_reset();
     } else if (bit_istrue(pin,bit(CYCLE_START_BIT))) {
-      bit_true(sys.rt_exec_state, EXEC_CYCLE_START);
+      bit_true(sys_rt_exec_state, EXEC_CYCLE_START);
     #ifndef ENABLE_SAFETY_DOOR_INPUT_PIN
       } else if (bit_istrue(pin,bit(FEED_HOLD_BIT))) {
-        bit_true(sys.rt_exec_state, EXEC_FEED_HOLD); 
+        bit_true(sys_rt_exec_state, EXEC_FEED_HOLD); 
     #else
       } else if (bit_istrue(pin,bit(SAFETY_DOOR_BIT))) {
-        bit_true(sys.rt_exec_state, EXEC_SAFETY_DOOR);
+        bit_true(sys_rt_exec_state, EXEC_SAFETY_DOOR);
     #endif
     } 
   }
@@ -139,7 +139,7 @@ uint8_t system_execute_line(char *line)
             sys.state = STATE_IDLE;
             // Don't run startup script. Prevents stored moves in startup from causing accidents.
             if (system_check_safety_door_ajar()) { // Check safety door switch before returning.
-              bit_true(sys.rt_exec_state, EXEC_SAFETY_DOOR);
+              bit_true(sys_rt_exec_state, EXEC_SAFETY_DOOR);
               protocol_execute_realtime(); // Enter safety door mode.
             }
           } // Otherwise, no effect.
@@ -175,7 +175,7 @@ uint8_t system_execute_line(char *line)
             
             // TODO: Likely not required.
             if (system_check_safety_door_ajar()) { // Check safety door switch before homing.
-              bit_true(sys.rt_exec_state, EXEC_SAFETY_DOOR);
+              bit_true(sys_rt_exec_state, EXEC_SAFETY_DOOR);
               protocol_execute_realtime(); // Enter safety door mode.
             }
             
diff --git a/grbl/system.h b/grbl/system.h
index 94f2143..ee43ed2 100644
--- a/grbl/system.h
+++ b/grbl/system.h
@@ -72,20 +72,20 @@ typedef struct {
   uint8_t abort;                 // System abort flag. Forces exit back to main loop for reset.
   uint8_t state;                 // Tracks the current state of Grbl.
   uint8_t suspend;               // System suspend bitflag variable that manages holds, cancels, and safety door.
-
-  volatile uint8_t rt_exec_state;  // Global realtime executor bitflag variable for state management. See EXEC bitmasks.
-  volatile uint8_t rt_exec_alarm;  // Global realtime executor bitflag variable for setting various alarms.
-
+  
   int32_t position[N_AXIS];      // Real-time machine (aka home) position vector in steps. 
                                  // NOTE: This may need to be a volatile variable, if problems arise.                             
 
-  uint8_t homing_axis_lock;       // Locks axes when limits engage. Used as an axis motion mask in the stepper ISR.
-  volatile uint8_t probe_state;   // Probing state value.  Used to coordinate the probing cycle with stepper ISR.
   int32_t probe_position[N_AXIS]; // Last probe position in machine coordinates and steps.
   uint8_t probe_succeeded;        // Tracks if last probing cycle was successful.
+  uint8_t homing_axis_lock;       // Locks axes when limits engage. Used as an axis motion mask in the stepper ISR.
 } system_t;
 extern system_t sys;
 
+volatile uint8_t sys_probe_state;   // Probing state value.  Used to coordinate the probing cycle with stepper ISR.
+volatile uint8_t sys_rt_exec_state;  // Global realtime executor bitflag variable for state management. See EXEC bitmasks.
+volatile uint8_t sys_rt_exec_alarm;  // Global realtime executor bitflag variable for setting various alarms.
+
 
 // Initialize the serial protocol
 void system_init();