Best way to structure a source code tree

While not directly related to any docbook app, this is a question I'm struggling with as a beginner: how do I structure the source code tree for my article/book/etc.?

For example, we publish a manual with five chapters, eight appendices, and a sprinkling of images.

Is there a best practice for structuring the source? I mean, I could just mirror the way that TDG is structured, but I would really like to understand *why* it's structured that way. And also to understand why there are subtle differences between the structure of the current TDG and TDG5:

http://cvs.sourceforge.net/viewcvs.py/docbook/defguide/
http://cvs.sourceforge.net/viewcvs.py/docbook/defguide5/

Does my question make any sense at all? Any pointers would be *greatly* appreciated.

Thanks,

Mike