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Adding custom PWM output to extruder

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I would like to add a preset to an extruder such as in Repetier's color mixing and virtual extruders definitions, but with the pwm output instructions going to a set of auxiliary pwm pins. Would anyone have any advice on how I might edit pins to create that output? So far I am putting pieces together to try and cobble that, either by adding a custom MCode entry or editing the output of M163 such as is used by the Repetier virtual extruder.

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