ardupilot/Tools/APM2_2560_bootloader/FLASH.txt

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to build the hex:
make mega2560
To flash the firmware, use avrdude version 5.11 or above
SERIAL_PORT=/dev/tty.usbserial
# erase the chip (necessary before unlocking can happen), then unlock the boot loader area
avrdude -e -c stk500v2 -p m2560 -P $SERIAL_PORT -U lock:w:0x3f:m
# flash the hex file (whatever.hex)
avrdude -v -c stk500v2 -p m2560 -P $SERIAL_PORT -U flash:w:stk500boot_v2_mega2560.hex
# re-lock the bootloader area of the chip
avrdude -c stk500v2 -p m2560 -P $SERIAL_PORT -U lock:w:0x0f:m