[WillAdams]

Sounds like a job for "Literate Programming":

http://literateprogramming.com/

I couldn't easily count the number of re-writes for my current project, but it keeps getting better, and each new iteration has had an updated architecture allowing for new features. When I re-wrote it as a Literate Program (first a .dtx, now a "normal" .tex) things got much more expressive and easier to work with.