Haha, I'm actually working on that too! Currently experimenting with a graph based editor.

Also, you might like The Fieldstone Method (Weinberg).

PS. Andy Matuschak's notes: http://notes.andymatuschak.org have some good tips on a similar subject. (My "digital garden" is more of a choose your own adventure book, I'm not married to a single methodology, but I appreciate much of their work)