I have uploaded the basic Shagmatic firmware to Githib. I am not at home so I can not test it on a real machine but there is no reason to believe that I screwed anything up. The only simplification was to remove the board test procedure. I added comments and got rid of most of the obsolete code. The link to the Github repository is on the resource page.
I recommend using the compiled binary, that has been tested, for use on Shagmatic boards at least until I can test the Github version.
I hope that releasing the firmware as open source will encourage others to extend the functionality in a variety of ways. I need to write a doc that explains how to interface with the Shagmatic board firmware via the input and output pins.