Here are the Github links for the source code used in this project.  If you want to go a-hacking, you will most likely want the Launcher firmware.  The bootloader code is included for those who are interested, but it's not needed unless you are starting out with a factory-fresh chip.  After the initial bootloader flashing, all further flashing of firmware, etc is done either through Arduino, or better yet - by dropping a UF2 file onto the USB device itself.  (Double click reset to open the USB firmware drive for drag & drop flashing)

Launcher Firmware Source Code (Arduino Sketch)

https://github.com/electronrancher/sam-fusee-launcher

Bootloader Source Code

https://github.com/electronrancher/uf2-samdx1