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So far the most popular bootloaders for ATxmega seem to be AVR109. For USB bootloaders, then there are Microchip FLIP2 and Caterina (USB to Serial + AVR109). I've also encountered STK500v2 bootloaders.
I have not been able to get any bootloader working yet on my ATxmega32A4U breakout board with FT232RL. I need to try again.
urboot for AVR xMega will be interesting.
From here.
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