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When Fran did the rewrite of the original software, he used a Linux build environment. I don't think I've ever successfully tried to compile the code in AVR Studio. Part of the issue was that AVR Studio had a problem with putting the hex file in a different part of memory than normal, because there was a bootloader. So, each time I make a code change, I log out of windows, log in to ubuntu linux, make changes, compile them, send hex files to my email, and log back out and try them.
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