Trevor
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I suppose that would a matter to dissolve somehwere at the very end, probably requiring some hardware modification such as adding a resistor between two pins to provide a high/low/off setting, or re-routing/bridging some pins as to connect it to a hardware-pwm capable output.
I don't have the circuit design handy, but if I recall correctly I believe there are only one or two pins that are PWM capable, and they are used for other things. I also am pretty sure most if not all pins are used.
That being said, the whole point of the project is to improve upon the platform without making any hardware modifications.
As for reprogramming: isn't it possible to use a ICSP clamp connector to reprogram the uC using any USB powered programmer?
I just pop the chip out, program it, then socket it again.
Trevor