I'm new here and probably raving about something everyone else already knows but have you seen
http://phpxref.com/xref/zencart/nav.html.gz?index.php.source.html.gz

It's a zen cart 1.3.0.1 source code index!! Wow!
Probably outdated but still pretty helpful.

I think this or something like it should be linked into the Zen website in an obvious place.

If anyone knows of something better, please let me know.