Just an FYI: I successfully programmed an Arduino Due (SAM ARM-based)
using the Debian-packaged version of the Arduino IDE. The board support
information is now controlled through the "Boards Manager" feature,
which will independently install support into the ~/.arduino15 folder
regardless of what the Debian package comes with.
That said, this bug is probably still valid for ADK devices. I don't own
one of those boards to test.
Ryan