Hi Robert,
The way I approached this for my project is as follows. I have a dummy Harmony 3 project where I configure the peripherals and generate code and a separate project where I have my application code with FreeRTOS. When I need to access a new peripheral, as I add functionality/ debug another section of the target, I go to the dummy project, configure the peripheral to my requirements, generate the code and copy it across to my application code base.
If there are any ISRs, I modify as per our other thread.
It’s far from ideal, but it stops having to review the code merge every time I add a peripheral/library to the project.