In reply to:

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There ought to be a Unix console serial upgrader somewhere. All the code you need is in the emptool sources, in lib/protocol/upgrader.cpp. I think you'll need to write a main() for it, though.

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I think upgclient is one of the things that gets built from the emptool sources - i.e. the main() is provided. It's a while since I built it, though - and next time I'll probably upgrade around Hijack using mlord's via-ethernet upgrader.