Okay, so there are two ways to go about this.
But first, a note: do not use RepG to upload the firmware, it’ll be better to use one of the following methods.
The first step for both ways requires you to download the firmware’s .hex file.
Here’s the file for the atmega2560 mightyboard’s firmware version 7.7: http://jettyfirmware.yolasite.com/resources/release/firmware/mighty\_one-2560-Sailfish-v7.7.0-r1432.hex
You can also search this xml file to find direct download links to all the sailfish firmwares: http://jettyfirmware.yolasite.com/resources/release/firmware.xml (just replace the “firmware.xml” in the url with whatever is in the “relpath” section of the xml for the firmware you want)
By the way, I’d suggest unplugging the heating bed before continuing, it’s probably safer if you do.
Anyways, here are your two options: USB or ICSP. I can only attest to ICSP being more reliable, though.
To upload over USB, you’ll hook up the printer over USB and use AVRDUDE to flash whatever com port the printer is on. Make sure the programmer option is STK500v2. Also you may need to hit the reset button in the back of the printer when you start AVRDUDE in Command Prompt. I’m not sure on that front because I had screwed up my ability to perform the this method so I needed to use second one.
To upload via ICSP, you’ll need an AVR programmer that can flash a memory size of up to 256 Kb. The atmel avrisp mkII should work: Amazon.com
You need to open up the bottom of the printer and attach the programmer to the ISP port for the atmega2560 chip. You then flash the memory using AVRDUDE again. Also make sure AVRDUDE is using the correct programmer setting (it should be avrisp2 or something like that). (You can try atmel studio too, but I haven’t tried it so I can’t say how well it works).
If you try over USB first and it doesn’t work and the printer stops working all together (I don’t mean that it won’t turn on, I mean that it ends up with a blank LCD screen), then you’ll need to use the ICSP option to fix the printer.
You can also try and find a cheaper AVR programmer, just make sure it can support a flash size of up to 256 kb!
FINAL NOTE: If you didn’t understand any part of what I said, then do not try to do anything without performing significant research first. If you jump into this without enough understanding, you risk bricking your printer.