I can relate to the Harmony issues. I had a similar issue recently getting mTouch (capacitive button sensing) to work on a PIC16F.
First, I purchased a low-cost Curiosity dev kit because it has an mTouch button on it. The factory firmware works perfectly well with this board, cap sensor lights the LED when pressed and all that. So, you'd suppose this factory demo application would be available on Microchip's website? Nope! Searched for a good half hour before giving in. None of the demo applications for other processors support it either!
So, I decide to overwrite the firmware and replace it with new software using the mTouch library. First, it turned out my JRE for MPLAB X was out of date so I had to manually replace the JRE and change a configuration file. Then, I had to faff around with getting Microchip's Code Generator working because no, you can't use mTouch without that, it would be too easy. Finally, I do all of this and it does pulse the pin but because the interrupts aren't configured correctly, it doesn't work for detecting presses. Not to mention it uses something like 99% of the CPU with my main loop barely getting a chance to execute! I'm four hours in the hole and making no progress. So, in the next half hour I knock together a simple CapTouch library of my own which works perfectly. Microchip throw over 1,000 lines at the problem and produce a barely functional library: 50 lines later I have a simple capacitive touch sensor, which is all I wanted. Why do they make it so abstracted and complex?? It's a f**king 8-bit processor with 512 bytes of RAM and a few K's of flash...It doesn't need abstraction, it can't handle it!
Microchip just screw up software. They just can't write decent software for their own CPUs!