Programming Due through Rasp Pi - Or other Options

Hi Folks,

I have a rather complex project consisting of the following:

Arduino Due Master - controls gps and main sensor functions
Arduino Due Motor Controller - in control of 3 steppers and 1 dc motor, 3 IMUs
Raspberry Pi - Webserver for remote control and data feedback

My communications are set up as follows:

Pi <->Master<->MotorController

Through serial connections.

It’s working well but now I need to future proof. Ideally I want to be able to remotely reprogramme the Arduino Dues, taking advantage of the Pi already in the system. I’ve been working with Arduinos for a year now, great little platforms, but my Pi knowledge is non-existent (always eager to learn). My thoughts are that by compiling on PC, I can upload the .bin/hex/whatever to the Pi and have it transmit to the correct Due through the serial (I plan to use this forum post for the Due memory clear -

The reason I’m on this forum is that the Arduino Dues, as great as they are, require a seperate uploader/programmer (BOSSA) instead of AVRDude and I can’t find any way to run it on the Pi. I’m looking for some advice as to whether this is the best approach and, if so, is there any way I can port the Bossac over to the Pi?