Lots of re-organization and cleaning-up. Some bug fixes.

- Added a new source and header file called system. These files contain
the system commands and variables, as well as all of the system headers
and standard libraries Grbl uses. Centralizing some of the code.

- Re-organized the include headers throughout the source code.

- ENABLE_M7 define was missing from config.h. Now there.

- SPINDLE_MAX_RPM and SPINDLE_MIN_RPM now defined in config.h. No
uncommenting to prevent user issues. Minimum spindle RPM now provides
the lower, near 0V, scale adjustment, i.e. some spindles can go really
slow so why use up our 256 voltage bins for them?

- Remove some persistent variables from coolant and spindle control.
They were redundant.

- Removed a VARIABLE_SPINDLE define in cpu_map.h that shouldn’t have
been there.

- Changed the DEFAULT_ARC_TOLERANCE to 0.002mm to improve arc tracing.
Before we had issues with performance, no longer.

- Fixed a bug with the hard limits and the software debounce feature
enabled. The invert limit pin setting wasn’t honored.

- Fixed a bug with the homing direction mask. Now is like it used to
be. At least for now.

- Re-organized main.c to serve as only as the reset/initialization
routine. Makes things a little bit clearer in terms of execution
procedures.

- Re-organized protocol.c as the overall master control unit for
execution procedures. Not quite there yet, but starting to make a
little more sense in how things are run.

- Removed updating of old settings records. So many new settings have
been added that it’s not worth adding the code to migrate old user
settings.

- Tweaked spindle_control.c a bit and made it more clear and consistent
with other parts of Grbl.

- Tweaked the stepper disable bit code in stepper.c. Requires less
flash memory.

stepper.c

@@ -19,12 +19,11 @@
   along with Grbl.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-#include <avr/interrupt.h>
+#include "system.h"
+#include "nuts_bolts.h"
 #include "stepper.h"
-#include "config.h"
 #include "settings.h"
 #include "planner.h"
-#include "nuts_bolts.h"
 
 
 // Some useful constants.
@@ -43,7 +42,7 @@
 // NOTE: Current settings are set to overdrive the ISR to no more than 16kHz, balancing CPU overhead
 // and timer accuracy.  Do not alter these settings unless you know what you are doing.
 #define MAX_AMASS_LEVEL 3
-// AMASS_LEVEL0: Normal operation. No AMASS. No upper cutoff frequency.
+// AMASS_LEVEL0: Normal operation. No AMASS. No upper cutoff frequency. Starts at LEVEL1 cutoff frequency.
 #define AMASS_LEVEL1 (F_CPU/8000) // Over-drives ISR (x2). Defined as F_CPU/(Cutoff frequency in Hz)
 #define AMASS_LEVEL2 (F_CPU/4000) // Over-drives ISR (x4)
 #define AMASS_LEVEL3 (F_CPU/2000) // Over-drives ISR (x8)
@@ -182,12 +181,10 @@ static st_prep_t prep;
 // enabled. Startup init and limits call this function but shouldn't start the cycle.
 void st_wake_up() 
 {
-  // Enable steppers by resetting the stepper disable port
-  if (bit_istrue(settings.flags,BITFLAG_INVERT_ST_ENABLE)) { 
-    STEPPERS_DISABLE_PORT |= (1<<STEPPERS_DISABLE_BIT); 
-  } else { 
-    STEPPERS_DISABLE_PORT &= ~(1<<STEPPERS_DISABLE_BIT);
-  }
+  // Enable stepper drivers.
+  if (bit_istrue(settings.flags,BITFLAG_INVERT_ST_ENABLE)) { STEPPERS_DISABLE_PORT |= (1<<STEPPERS_DISABLE_BIT); }
+  else { STEPPERS_DISABLE_PORT &= ~(1<<STEPPERS_DISABLE_BIT); }
+
   if (sys.state & (STATE_CYCLE | STATE_HOMING)){
     // Initialize stepper output bits
     st.dir_outbits = settings.dir_invert_mask; 
@@ -217,18 +214,18 @@ void st_go_idle()
   // Disable Timer1 Stepper Driver Interrupt. Allow Timer0 to finish. It will disable itself.
   TIMSK1 &= ~(1<<OCIE1A); 
   busy = false;
-
-  // Disable steppers only upon system alarm activated or by user setting to not be kept enabled.
+  
+  // Set stepper driver idle state, disabled or enabled, depending on settings and circumstances.
+  bool pin_state = false;
   if (((settings.stepper_idle_lock_time != 0xff) || bit_istrue(sys.execute,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);
-    if (bit_istrue(settings.flags,BITFLAG_INVERT_ST_ENABLE)) { 
-      STEPPERS_DISABLE_PORT &= ~(1<<STEPPERS_DISABLE_BIT); 
-    } else { 
-      STEPPERS_DISABLE_PORT |= (1<<STEPPERS_DISABLE_BIT); 
-    }   
+    pin_state = true;
   }
+  if (bit_istrue(settings.flags,BITFLAG_INVERT_ST_ENABLE)) { pin_state = !pin_state; }
+  if (pin_state) { STEPPERS_DISABLE_PORT |= (1<<STEPPERS_DISABLE_BIT); }
+  else { STEPPERS_DISABLE_PORT &= ~(1<<STEPPERS_DISABLE_BIT); }
 }
 
 
@@ -429,11 +426,14 @@ void st_reset()
   segment_buffer_head = 0; // empty = tail
   segment_next_head = 1;
   busy = false;
+  
+  // Initialize stepper driver idle state.
+  st_go_idle();
 }
 
 
 // Initialize and start the stepper motor subsystem
-void st_init()
+void stepper_init()
 {
   // Configure step and direction interface pins
   STEPPING_DDR |= STEP_MASK;
@@ -450,7 +450,8 @@ void st_init()
   TCCR1A &= ~(3<<COM1A0); // output mode = 00 (disconnected)
   TCCR1A &= ~(3<<COM1B0); 
   TCCR1B = (TCCR1B & ~(0x07<<CS10)) | (1<<CS10);
-
+  // TIMSK1 &= ~(1<<OCIE1A);  // Timer 1 disabled in st_go_idle().
+  
   // Configure Timer 0: Stepper Port Reset Interrupt
   TIMSK0 &= ~(1<<TOIE0);
   TCCR0A = 0; // Normal operation
@@ -459,12 +460,8 @@ void st_init()
   #ifdef STEP_PULSE_DELAY
     TIMSK0 |= (1<<OCIE0A); // Enable Timer0 Compare Match A interrupt
   #endif
-
-  // Start in the idle state, but first wake up to check for keep steppers enabled option.
-  st_wake_up();
-  st_go_idle();
 }
-
+  
 
 // Planner external interface to start stepper interrupt and execute the blocks in queue. Called
 // by the main program functions: planner auto-start and run-time command execution.
@@ -666,8 +663,8 @@ void st_prep_buffer()
       the end of planner block (typical) or mid-block at the end of a forced deceleration, 
       such as from a feed hold.
     */
-    float dt_max = DT_SEGMENT;
-    float dt = 0.0;
+    float dt_max = DT_SEGMENT; // Set maximum segment time
+    float dt = 0.0; // Initialize segment time
     float mm_remaining = pl_block->millimeters;
     float time_var = dt_max; // Time worker variable
     float mm_var; // mm-Distance worker variable
@@ -676,8 +673,8 @@ void st_prep_buffer()
       switch (prep.ramp_type) {
         case RAMP_ACCEL: 
           // NOTE: Acceleration ramp only computes during first do-while loop.
-          speed_var = pl_block->acceleration*dt_max;
-          mm_remaining -= dt_max*(prep.current_speed + 0.5*speed_var);
+          speed_var = pl_block->acceleration*time_var;
+          mm_remaining -= time_var*(prep.current_speed + 0.5*speed_var);
           if (mm_remaining < prep.accelerate_until) { // End of acceleration ramp.
             // Acceleration-cruise, acceleration-deceleration ramp junction, or end of block.
             mm_remaining = prep.accelerate_until; // NOTE: 0.0 at EOB
@@ -718,10 +715,14 @@ void st_prep_buffer()
       }
       dt += time_var; // Add computed ramp time to total segment time.
       if (dt < dt_max) { time_var = dt_max - dt; } // **Incomplete** At ramp junction.
-      else if (mm_remaining > prep.minimum_mm) { // Check for slow segments with zero steps.
-        dt_max += DT_SEGMENT; // Increase segment time to ensure at least one step in segment.
-        time_var = dt_max - dt;
-      } else { break; } // **Complete** Exit loop. Segment execution time maxed.
+      else {
+        if (mm_remaining > prep.minimum_mm) { // Check for slow segments with zero steps.
+          dt_max += DT_SEGMENT; // Increase segment time to ensure at least one step in segment.
+          time_var = dt_max - dt;
+        } else { 
+          break; // **Complete** Exit loop. Segment execution time maxed.
+        }
+      }
     } while (mm_remaining > prep.mm_complete); // **Complete** Exit loop. Profile complete.
    
     /* -----------------------------------------------------------------------------------
@@ -745,7 +746,7 @@ void st_prep_buffer()
     
     #ifdef ADAPTIVE_MULTI_AXIS_STEP_SMOOTHING        
       // Compute step timing and multi-axis smoothing level.
-      // NOTE: Only one prescalar is required with AMASS enabled.
+      // NOTE: AMASS overdrives the timer with each level, so only one prescalar is required.
       if (cycles < AMASS_LEVEL1) { prep_segment->amass_level = 0; }
       else {
         if (cycles < AMASS_LEVEL2) { prep_segment->amass_level = 1; }