The bootloader on the chipKIT is based on the same bootloader that I developed for the mega2560. It uses stk500v2 protocol.
Avrdude can be used from the command line with the chipKIT boards or any other board that has the bootloader installed The command would be something like this >avrude -c stk500v2 -p pic32 -P /dev/tty.usbmodem1234 -b 115200 -U flash:w:filename.hex Or, under Windows(If you've copied avrdude.exe and avrdude.conf into the MPLABX bin folder): "C:\Program Files\Microchip\MPLABX\mplab_ide\bin\avrdude.exe" -C"C:\Program Files\Microchip\MPLABX\mplab_ide\bin\avrdude.conf" -v -p32MX795F512L -cstk500v2 -P COM40 -b 115200 -U flash:w:pic32_template_1.production.hex
When using mpide, default is to remove all the intermediate files between the mpide source of your project (.mpe file) and code uploaded on the chipKIT. But all the files generated by mpide (including the hex file) can be kept by changing mpide preference file. From Linux:
Now, all temporary files from build command will be kept. To locate the right directory with your build, from mpide, press the "shift" key while starting the build/verify command. You will have details about the build process (commands, outputs, path ...) in mpide output console. Example:
/opt/mpide-0023-linux32-20111221/hardware/pic32/compiler/pic32-tools/bin/pic32-g++  -O2  -c  -mno-smart-io  -w  -fno-exceptions  -ffunction-sections  -fdata-sections  -G1024  -g  -mdebugger  -Wcast-align  -mprocessor=32MX320F128H  -DF_CPU=80000000L  -DARDUINO=23  -D_BOARD_UNO_  -Danything_you_want  -Danything=1   -I/home/fred/Arduino/Serial2   -I/opt/mpide-0023-linux32-20111221/hardware/pic32/cores/pic32   -I/opt/mpide-0023-linux32-20111221/hardware/pic32/variants/Uno32    /tmp/build6773645236763377018.tmp/Serial2.cpp  -o  /tmp/build6773645236763377018.tmp/Serial2.cpp.o
...
/opt/mpide-0023-linux32-20111221/hardware/pic32/compiler/pic32-tools/bin/pic32-ar  rcs  /tmp/build6773645236763377018.tmp/core.a  /tmp/build6773645236763377018.tmp/main.cpp.o
/opt/mpide-0023-linux32-20111221/hardware/pic32/compiler/pic32-tools/bin/pic32-g++  -Os  -Wl,--gc-sections  -mdebugger  -mprocessor=32MX320F128H  -o  /tmp/build6773645236763377018.tmp/Serial2.cpp.elf  /tmp/build6773645236763377018.tmp/Serial2.cpp.o    /tmp/build6773645236763377018.tmp/core.a  -L/tmp/build6773645236763377018.tmp  -lm  -T  /opt/mpide-0023-linux32-20111221/hardware/pic32/cores/pic32/chipKIT-UNO32-application-32MX320F128L.ld
/opt/mpide-0023-linux32-20111221/hardware/pic32/compiler/pic32-tools/bin/pic32-objcopy  -O  ihex  -j  .eeprom  --set-section-flags=.eeprom=alloc,load  --no-change-warnings  --change-section-lma  .eeprom=0  /tmp/build6773645236763377018.tmp/Serial2.cpp.elf  /tmp/build6773645236763377018.tmp/Serial2.cpp.eep
/opt/mpide-0023-linux32-20111221/hardware/pic32/compiler/pic32-tools/bin/pic32-bin2hex  -a  /tmp/build6773645236763377018.tmp/Serial2.cpp.elf
Binary sketch size: 10748 bytes (of a 126976 byte maximum)
WARNING: the temporary directory will be removed when mpide will be closed. You have to backup the hex file before closing mpide. To go back to initial configuration (files removed after each build), just set the preproc.save_build_files attribute to false
preproc.save_build_files=false
copy avrdude.conf file from mpide to ~/.avrduderc, example:
cp /opt/mpide-0023-linux32-20111221/hardware/tools/avrdude.conf ~/.avrdude.rc
Use ever avrdude from mpide or from your own Linux distro... Here are details about avrdude from Ubuntu Precise Penguin:
dpkg-query -l avrdude
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                             Version                          Description
+++-================================-================================-================================================================================
ii  avrdude                          5.11.1-1                         software for programming Atmel AVR microcontrollers
Check if the avrdude configuration file from mpide is used, and which PIC32 devices are available:
fred@kat:~/MPLABXProjects/Blink$ avrdude -p ?
Valid parts are:
  pic32-440 = 32MX440F512H    [/home/fred/.avrduderc:16438]
  pic32-460 = 32MX460F512L    [/home/fred/.avrduderc:16251]
  pic32-360 = 32MX320F128H    [/home/fred/.avrduderc:16054]
  pic32-360 = 32MX320F064H    [/home/fred/.avrduderc:15863]
  pic32-360 = 32MX360F512L    [/home/fred/.avrduderc:15672]
  pic32 = 32MX795F512L    [/home/fred/.avrduderc:15483]
...
We can see that pic32-360 has to be used for Uno32 (32MX320F128H) Example, with:
fred@kat:~/MPLABXProjects$ avrdude -P /dev/ttyUSB0 -p pic32-360  -b 115200 -c stk500v2 -v -v -U flash:w:Haribo.cpp.hex
avrdude: Version 5.11.1, compiled on Oct 30 2011 at 10:37:28
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch
         System wide configuration file is "/etc/avrdude.conf"
         User configuration file is "/home/fred/.avrduderc"
         Using Port                    : /dev/ttyUSB0
         Using Programmer              : stk500v2
         Overriding Baud Rate          : 115200
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
Oops... Upload error ? I have to press the Uno32 reset button, then code is uploaded:
         AVR Part                      : 32MX320F128H
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
           flash         65    10   256    0 yes    131072  256    512  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00
         Programmer Type : STK500V2
         Description     : Atmel STK500 Version 2.x firmware
         Programmer Model: AVRISP
         Hardware Version: 15
         Firmware Version Master : 2.10
         Vtarget         : 0.0 V
         SCK period      : 0.1 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x504943
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
avrdude: current erase-rewrite cycle count is -1145324613 (if being tracked)
avrdude: erasing chip
avrdude: reading input file "Haribo.cpp.hex"
avrdude: input file Haribo.cpp.hex auto detected as Intel Hex
avrdude: writing flash (32664 bytes):
Writing | ################################################## | 100% 9.15s
avrdude: 32664 bytes of flash written
avrdude: verifying flash memory against Haribo.cpp.hex:
avrdude: load data flash data from input file Haribo.cpp.hex:
avrdude: input file Haribo.cpp.hex auto detected as Intel Hex
avrdude: input file Haribo.cpp.hex contains 32664 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 3.29s
avrdude: verifying ...
avrdude: 32664 bytes of flash verified
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: safemode: Fuses OK
avrdude done.  Thank you.
To use avrdude to upload a hex file you just built in MPLAB X, there are a couple steps you need to follow:
If all of the paths are set up properly, you should get an automatic download every time you rebuild your project in MPLABX. Many times, I need to reset my chipKIT board in order to get the download to work, even though I don't need to do this when using MPIDE. I'm not sure why this is - if anyone can suggest a workaround, that would really help.