You can try to connect an SD card interface to your Mini Breakout Board, in which case I would suggest you check the Schematic of the Arduino Expansion Board, specifically the
section for the SD card. There’s a thread already opened where this is discussed https://communities.intel.com/thread/68367.
You can also try increasing the size of “root” as you already stated. According to this thread https://communities.intel.com/thread/55612, you can adjust the size of the partitions.
I've added all the prerequisite libraries into the repo, as well as Node.js 0.12.x. The approach used in referenced scripts/blogs installs Cloud9 SDK on top of that and then runs the server out of it, which communicates to the Cloud9 cloud. I don't think it makes sense to package this piece, because they are using a shell script as an official install method and it essentially downloads and installs a bunch of npm modules - which as easily done by using the script itself as using opkg, or maybe even easier, as npm handles a lot of stuff automatically.