The MCU can only be programmed through Eclipse (MCU SDK). All the information available about using the MCU can be found here: Creating applications with the MCU SDK for the Intel® Edison board | Intel® Developer Zone
That makes me sad and a bit surprised, why wouldn't a shell interface to the compiler and programmer be made available? This way the MCU can't be programmed from the Edison itself, which seems strange to me since that's one of the biggest advantages with having the MCU on-board. I might want to switch or modify what's run on the Quark out in the real world without having access to a specific computer specifically set up with Eclipse and the SDK to work with my Edison. Ah well, thank you very much for the answer!