Konrad, I'm so happy you touched my sick theme from few months. Here is no spindle at all. But... almost all adequate CAM software hearing mill knows rotate tool. Especially checked SolidCAM. Next step to take a look to mastercam. In any case I'll cheat the software, but this is slow solution.
The described behavior has a lot of application. BTW if the stepper drivers are smart and checks the current in windings they will know is the step actually goes or not. Hold the step with the trigger until it done (some timeout, possible to done never) logic AND from all steppers and HOLD until all rest steps are present will prepare closed loop steppers.
For servos situation is bit different, but if one good guy has understood what I have talked, soon servo drivers will have two different pulse dependable closed loop controls. Unfortunately, for now I can't explain more about this feature, because I don't know will he does this or not.
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Hood, no buttons. This will be absolutely automatic solution. How often and how many times will present the "not ready" condition knows no one. Stupid is to stay near the machine to wait if this present or not. Also, temperature depends from what part of the tool is in use right now. High temperature will compensate with low heating PWM, low one ... only with no movement until it normalized. Temperature is provisional in this explanation. Every condition which you want and can resolve is suitable.
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Good is to know for missing deceleration. Important is to know after recovering machine starts on the same place with the rest of steps to done program line.