The GitHub version and the version on the jstat website are vastly different. Just thought I'd point that out. I like the way that the GitHub version is laid out in a modular format. Some of the functionality is different so you can't just switch from the old library to the GitHub version and expect all the code to work.
You're absolutely correct. If you look at the commit history, you'll see that it started out as two different projects. We noticed we had the same goals and decided to combine projects. I've been in charge of architecting the API since then.
One of my goals was to make it very modular and easily extendable. In the overview page of the documentation I explain how this was accomplished (http://jstat.github.com/overview.html)
