So there are currently 2 versions of the software in our github repo. The gro-microcontroller code is from the first version. If you want to use that on the arduino, you should run gro-controller on the RPi and use gro-ui to view your data. The Pi image @JamesO mentioned is for running gro-controller on the Pi.
The docker setup is for the new version of the software which is still under development. In particular, it is for installing the openag_brain code on the Pi. I'll probably tag a semi-stable version of the code within a few weeks with better installation instructions. For this codebase, you configure a set of firmware modules through CouchDB and the RPi automatically flashes the Arduino with code to interface with the hardware. There is a UI for it in the openag_ui repo that is also still in flux.
So for now you're probably better off using the Pi image linked to here at least until we release the new version of the software.