Is there any reason you would have to do any updates to code other than the normal updates via the gui or arduino interface to the oilpan or the mega? I noticed a hex file the other day mentioned. If so what is process. I have a mega and latest oilpan.
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If you wanna use channel 8 on a multicopter you would have to update the firmware of the ppm encoder.
http://code.google.com/p/ardupilot-mega/wiki/Encoder