I have successfully compiled my program, and try to upload it to the Arduino Due using BOSSAC (arduino/hardware/tools/bossac.exe). The problem is I get this error:
No device found on /dev/ttyACM0
This is the argument I use to specify the port:
--port=/dev/ttyACM0
It works in the Arduino IDE. I've tried both giving rw to others and running BOSSAC as root.