I have a stack consisting of RPi 2, Arduberry, Arduino Motor Shield R3. The only way I can upload new code to the Arduberry is to remove the motor shield. Otherwise I get:
avrdude: The AVR device is not responding avrdude: initialization failed rc=-1 Double check connections and try again, or use -F to override this check.
I did some experimenting and if anything is plugged into pin 13, I get this error. Is there any way to update the code on an Arduberry without removing a shield?