alphaomega
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I have a couple old PC wiring harnesses laying around. Is there any reason I couldn't use one of the four wire connectors to solder in a permanent header to both the STC and the Arduino? That way you just clip it in if you need to flash. And, no cost.
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One reason might be that you need 5 wires. You could get by with 4 if you allow target to supply power (i.e. skip 5v line and instead have STC-1000 provide power from mains), but you'll have to decide yourself if you are willing to do that (personally I would want to avoid it).