Dennis Welbourn wrote:
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...the AVRs are programmed through an SPI port and thus require a separate header and possible design considerations to separate ISP from normal functioning.

I wonder if something like the UART/SPI connection arrangement referenced here would work for AVRs too:

http://www.8052.com/users/dhenry

That could eliminate the separate header and separate parallel port programming cable, but you don't get a pretty GUI to use :-(