I was trying to update the firmware but when I compiled the program it was giving a bunch of ' 'xyz' not declared in this scope' errors. I'm not sure if I'm missing any files but I added the DS3231 and Time libraries that were included in the github download.
In general, the libraries have to be in the right place, and that depends on the OS you are using. There's a great HowTo here:
and especially look at the "Manual Installation" section.
If you are really adventurous, you might want to look at the Git master, where all the weird stuff goes on (a bit quiet at the moment, but it will liven up again soon):