If someone wonders why the board is booted like that, and what is that baud rate 1200 hack, or would like to build their own firmware without using Arduino. I have a little write-up of my findings, explaining how things are booted and flashed on Arduino Due/SAM3X in the playground - here: Arduino P…

Arduino Due bootloader explained

graynomad April 13, 2013, 1:50am 3

No it won't work with a SAM, I think he's referring to modifying the ATMEGA16U2 code.

Rob