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.

planner.c

@@ -249,19 +249,6 @@ uint8_t plan_check_full_buffer()
 }
 
 
-// Block until all buffered steps are executed or in a cycle state. Works with feed hold
-// during a synchronize call, if it should happen. Also, waits for clean cycle end.
-void plan_synchronize()
-{
-  // Check and set auto start to resume cycle after synchronize and caller completes.
-  if (sys.state == STATE_CYCLE) { sys.auto_start = true; }
-  while (plan_get_current_block() || (sys.state == STATE_CYCLE)) { 
-    protocol_execute_runtime();   // Check and execute run-time commands
-    if (sys.abort) { return; } // Check for system abort
-  }    
-}
-
-
 /* Add a new linear movement to the buffer. target[N_AXIS] is the signed, absolute target position
    in millimeters. Feed rate specifies the speed of the motion. If feed rate is inverted, the feed
    rate is taken to mean "frequency" and would complete the operation in 1/feed_rate minutes.
@@ -373,7 +360,8 @@ void plan_buffer_line(float *target, float feed_rate, uint8_t invert_feed_rate)
     // NOTE: Computed without any expensive trig, sin() or acos(), by trig half angle identity of cos(theta).
     float sin_theta_d2 = sqrt(0.5*(1.0-junction_cos_theta)); // Trig half angle identity. Always positive.
 
-    // TODO: Acceleration used in calculation needs to be limited by the minimum of the two junctions. 
+    // TODO: Technically, the acceleration used in calculation needs to be limited by the minimum of the
+    // two junctions. However, this shouldn't be a significant problem except in extreme circumstances.
     block->max_junction_speed_sqr = max( MINIMUM_JUNCTION_SPEED*MINIMUM_JUNCTION_SPEED,
                                  (block->acceleration * settings.junction_deviation * sin_theta_d2)/(1.0-sin_theta_d2) );
   }