In my initial experience with the Clicker2 for PIC32MX and MPIDE, I found that the loaded program was lost during reset or after powering off. After the reset or when the power was applied back, the board was getting into bootloader mode and stayed there indefinitely.
Today I tried to perform a better emulation of the Digilent PRO MX4, and I used a USB UART click and the bootloader downloaded from the Digilent website. The results were great. Now when resetting the board it goes into bootloader mode for about 10 seconds, the LED connected to pin RB10 flashing. It then exits the bootloader and runs the latest program. Also I found that serialprint and serialprintln are working as expected. Note that the USB UART must be installed in socket #1 on the Clicker2 board for this to work.
Another nice thing is that the Clicker2 does not complain if the USB UART is removed after programming. It just flashes RB10 for 10 secs than runs the already loaded program.
Now I can really work with this and have the full benefits of the free MPIDE and I can reuse most of my Arduino code on the Clicker 2 for PIC32MX, albeit with the small price of adding the extra USB UART click board. Just bear in mind that RB10 (which corresponds to Arduino digital pin 64 / analog input A8) will flash during the bootloader process. My recommendation is to avoid the use of this pin.
Note: a mirrored copy of the MX4 bootloader is available here.