Can't help you with the CLI programmer but under Linux the standard MPLABX IPE will flash devices with a compatible hex file. I use the IDE with the custom compiler (MTI bare-metal) option to work on my port of the MIPS pic32 family to a PIC32MZEF dev board using the debug USB connection. A simple bash script does the make using the IDE menus.
https://github.com/nsaspook/RIOT/tree/PIC32MZEF PIC32MZ EF CURIOSITY DEVELOPMENT BOARD There are some 'work in progress' interrupt and DMA enabled drivers for the uart and spi that are being used to test a simple BTLE demo using the RN4020 BLE2 click module in a socket in the examples directory of my fork.