The PICkit 3 frimware is NOT your application firmware. This is the code that is loaded into the PICkit 3 that modifies its functionality for the project's selected device.
Open Project Properties window.
Select PICkit 3 under Categories.
Select Firmware from the Options Categories combo box
Auto or manual selection of memories and ranges to program: If you check this box, you can specify which firmware image MPLAB X should load in the box below.
Click in the right-hand text box to search for a firmware file (.jam) to associate with the emulator:
MPLAB X IDE automatically downloads the correct firmware for your selected device. Only change this setting if you are having issues.