ErgoDox Infinity

The Infinity is two completely independent keyboards, and needs to be flashed for the left and right halves seperately. To flash them:

Make sure you are in the top-level qmk_firmware directory
Build the firmware with make ergodox_infinity-keymapname
Plug in the left hand keyboard only.
Press the program button (back of keyboard, above thumb pad).
Install the firmware with sudo make ergodox_infinity-keymapname-dfu-util
Build right hand firmware with make ergodox_infinity-keymapname MASTER=right
Plug in the right hand keyboard only.
Press the program button (back of keyboard, above thumb pad).
Install the firmware with sudo make ergodox_infinity-keymapname-dfu-util MASTER=right

More information on the Infinity firmware is available in the TMK/chibios for Input Club Infinity Ergodox

Infinity Master/Two Halves

The Infinity is two completely independent keyboards, that can connect together. You have a few options in how you flash the firmware:

Flash the left half, rebuild the firmware with "MASTER=right" and then flash the right half. This allows you to plug in either half directly to the computer and is what the above instructions do.
Flash the left half, then flash the same firmware on the right. This only works when the left half is plugged directly to the computer and the keymap is mirrored. It saves the small extra step of rebuilding with "MASTER=right".
The same as the previous one but with "MASTER=right" when you build the firmware, then flash the same firmware to both halves. You just have to directly connect the right half to the computer.
For minor changes such as changing only the keymap without having updated any part of the firmware code itself, you can program only the MASTER half.
It is safest to program both halves though.