Updating the Sketch software and uploading a new sketch works.
Maybe the software I was using previously (JavaScript Johnny5) was not yet working with the Arduino Due?
After looking at the Johnny Five information, I am left to ask - WHY? WHY replace the Arduino IDE with a terminal-based command line interface? Certainly this is the antithesis of making Arduino easy to learn and use for newcomers. I believe this is what is causing the OP's confusion, as the Johnny Five system has removed him from the normal Arduino learning system.
the reason for javascript is that JS is becoming the main language for web related projects, and I'd like to experiment streaming information from the web to the arduino or vice-versa.
Hmm... still not sure if those JS libs support the Due, but also reading firmata with Main Page - Firmata is not giving back results.
thinking to switch to an Uno - or indeed go with Sketch first.