Ideally I'll get my C together and write a program for the empeg to run (launched from a picker menu or whatever) which will replace the user shell stuff

No, don't do that!

Your current design is better, since it doesn't need any third-party software installed on the Empeg. Just put the developer image on it and then your program works.

All your program needs to do is send the proper keystrokes to the serial port and parse the screens it gets back.

Okay, so it needs two cables (USB/Serial) connected instead of one. So what?

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Tony Fabris