Maybe someone here will be able to help, I have taken this as far as I can for now...
I'm developing a web portal based around JForum, and rathe than integration JForum into a CMS I'm extending it to become the CMS. Right now I have two directories in my work dir: jforum and crapaud.
jforum is the CVS tree and crapaud contains the jars, my code, custom config, and a symlink to src/net/jforum. The idea is that I can continue to base my stuff around updates in CVS.
Anyway, as it stands there are very few changes from the base code right now, and so crapaud is very close to jforum in content, with only DB changes, and few small things (I've subclassed JForum to Crapaud as my entry point.