This page describes how to setup MPLAB X as a development environment. MPLAB X can have some quirks which can trip up first time users.
Harmony is Microchip's hardware abstraction & middleware libraries. With the exception of the USB code, we use only the lower level hardware abstraction libraries (typically PLIB_*). Harmony is still fairly new and after examining some of the code, I (Simon) have concerns about code quality.
MPLAB X comes with a Harmony Configurator Plugin (MHC) which auto-generates the boiler plate code from a Harmony configuration.
When used with Harmony, the design of the MPLAB X build / configuration system makes it difficult to move a project's directory to a new location on the filesystem. In fact, by default, a project's configurations.xml file uses relative paths to Harmony!
This project is set up to assume Harmony 1.06 is installed in /opt/microchip/harmony/v1_06 . If this is not the case on your system you have two options:
First of all, read the MPLAB X Getting Started Guide. From within MPLAB X, choose File -> Open Project, and then select the firmware/ja-rule.X file. Once the project has loaded, you can perform a build (Run -> Build Project) and program your device.