Steve,

How would an external pull up and pull down resisters work? What
differentiates the startup state from a controlled assertion of the output?

Thanks,
Eric

You can use external pull-up and pull-down resistors to set pin state. 
I'm pretty sure that is the only way to set outputs the way you want during
early boot.  You can also use a relay or charge pump in the E-Stop chain -
that should prevent anything from happening on the machine before EMC is
running.



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