Thanks for the response.
I have access to an ICD3 which I used to program my blinky LED application. This worked as expected.
Correct, the factory bootloader and the harmony boot loader use different communication protocols. I am wanting to use the stk500v2 protocol implemented by Digilent because the command line programmer tool is available for Linux and because I don't always have access to the ICD3. The AN1388 bootloader that is implemented with the harmony configurator doesn't have a Linux client. Microchip did publish the windows source code along with the application note, but attempting to modify that seems to be just another hazard ridden path.
The pic32prog source on github mentions compatibility with an [USB] HID AN1388 boot loader. I might be able to make that work without hacking up the windows code or cutting myself on the sharp corners in the linker scripts. I think that this will be my experiment for the next time I get my hands on the ICD3.
I've been poking through the linker files provided by XC32, harmony, as well as those in the chipKIT core. I'm really a newb as far as linker scripts go. It is not obvious what changes are necessary for bootloader support and which changes are out of preference or compiler compatibility.
Can Digilent provide the linker script for the boot loader, documentation, or perhaps the source itself, to aid with this endeavor?