There are 2 steps to uploading new code to the Arduberry. First step is to compile a new firmware and second is to upload it. If you have access to the Arduino IDE, then you can use it to compile the firmware and if you do not have access to it and want to do it over the command line, then you can use INO. With both these step, the end result is a .hex or a .cpp.hex file is created, which is the actual firmware that has to burnt. Once you have the firmware, you can upload it easily to the arduberry from the command line using: avrdude -c gpio -p m328p -U flash:w:<firmware_name>.hex.
Do let us know if this helps.