Trying to track down some bugs in the multi-spindle patch I have found
this section of code.

master: 
https://github.com/LinuxCNC/linuxcnc/blob/master/src/emc/task/taskintf.cc#L1871
multispindle: 
https://github.com/LinuxCNC/linuxcnc/blob/andypugh/multispindle-master/src/emc/task/taskintf.cc#L1856

And with multispindle everything works a bit better with speed,
direction and brake commented out.

Does anyone know why that section of code is needed? what is it
synching to what?

The problem I am seeing is that an M3 followed by an M4 writes a
negative speed to emcStatus->motion.spindle[s].speed so that the
effect of M4 is to reverse speed. ie:
M3 S100 -> speed 100
M4 -> speed -100
M3 -> speed -100
M4 -> speed 100

Oddly I don't see this effect in the master branch, and I am not clear
why as the code ought to be broadly similar.

-- 
atp
"A motorcycle is a bicycle with a pandemonium attachment and is
designed for the especial use of mechanical geniuses, daredevils and
lunatics."
— George Fitch, Atlanta Constitution Newspaper, 1916

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