Very nicely done, I think it's an improvement over the current layout.
I do think a CGI-related section would be nice, since it's such a common topic. You may want to consider making it an "additional cross-reference" section; that is, keep the existing classification, but list the CGI-related nodes a second time in their own section. That would make more maintenance work, so I leave it to your judgement as to whether it's worth it.
Another thing to consider in the "more work but may be nice" category: a simple ranking of "beginner, intermediate, advanced" on each tutorial. For example, References Quick Reference is for quite a different audience than References. Since most of tutorials are in fact meant to be introductory, it may be simpler to just tag the advanced material with some sort of symbol.