stepconf's "Charge pump" output and "ESTOP in" don't make sense
together.  This configuration leads to the situation you describe.

Stepconf's "Charge pump" is an output activated when the PC is running
and you click the "estop reset" button or press F1; it deactivates if
you activate that button again.

With "ESTOP in" (i.e., you have a real external estop chain) the GUI
"estop" button has no function, but another consequence of this is that
the charge-pump.enable is never driven TRUE by anything.

When doing custom hal, you have other choices such as to use
amplifier-enable to turn on the charge pump, or to use the estop_latch
component so that F1 is still required to be pressed after the external
estop condition is removed, or to connect the enable input to the
charge-pump enable.

Jeff

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