Updated comments. Changed stepper variable names to be more understandable. Added step locking note.

- Updated config comments and stepper code comments for the new changes.

- Changed stepper algorithm variable names to be more understandable in
what they actually do.

- Added a stepper lock note in default.h per user request.

- Started some code layout in handling feed holds and refactoring the
homing routine to use the main stepper algorithm instead of a seperate
version.

protocol.c

@@ -104,7 +104,9 @@ ISR(PINOUT_INT_vect)
 // limit switches, or the main program.
 void protocol_execute_runtime()
 {
+  // Reload step segment buffer
   st_prep_buffer();
+  
   if (sys.execute) { // Enter only if any bit flag is true
     uint8_t rt_exec = sys.execute; // Avoid calling volatile multiple times