Intelligent Structure Question

Hey all

So, I have a tiny question, but one that has annoyed me enough I thought I’d open convo.

Currently, I user a brilliant theme created by a brilliant dev. I have modded it out heavily, added my own special sauce, including introducing several custom post types, taxonomies, and a number of other things. Here’s the dilemma:

I place a lot of these revisions in the themes Functions.php. Great. Accept that the person developing this theme is such a bad ass that he issues frequent improvements and I update frequently — Meaning, for each iteration, I reintroduce and debug all of my additions.

Is there an intelligent way to mix in my behaviors allowing the theme’s code-base to be an undoctored edition of the theme? I’d love each deployment of the theme to be sterile version of his theme release because if I am given an opportunity, every 4 days, to fuq it up, I certainly will. And often do, causing hours of debug. 🙂

Pardon, I’m pretty new at all this and wasn’t able to nail anything into the famed loop that successfully accomplished this. 🙂

s