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Programming the EEprom on the Experimenter's KIT

Team,

I am building a prototyping board that will drive a 100 HP motor. . .In the interest of saving time, I lifted my old MCU section and replaced it with an exact copy of the Experimenter's Kit.  I am looking forward to leveraging all of the extra pins on the Delfino.  BUT, I suspect that some of the handshaking between the KIT and CCS is stored in the on board prom.

How do I program that prom?  Through the USB appears to be a chicken and egg thing.  Through the Jtag? Hmmm.

Will Friesen