The PIC32 chipKit board is designed to use in an Arduino™ style environment called MPIDE (Multi Platform Integrated Development Environment).
The bootloader is the same bootloader as used in the Arduino™ Mega 2560 board. This bootloader uses STK500V2 protocol. Avrdude is used to talk to it.
In the normal Arduino™ environment you can use the Arduino™ IDE to burn the bootloader. It uses an ISP (In System Programmer) to do the actuall programming of the bootloader. PIC32 does not support the same style of ISP programmer and therefore cannot be used to burn the pic32 bootloader.
To program the bootloader on a PIC32 chip, you need to use an ICD or PicKit programmer. I use the ICD-3 but the PicKit-3 also works. This is done from MPLAB, the Microchip development environment. There are several versions. The new MPLAB-X is cross platform and can be downloaded free.
MPLAB-X on the Mac was used to develop the bootloader. The bootloader source and the MPLAB-X project will be on githup (as of May 22, 2011 it is not there yet).