Features / Usability

1) A Structure is a collection of interlinked wiki pages.
A Category is recursively nestable, and can have anything in it.
The left Nav Bar (when making a menu) to my knowledge only supports one level of nesting. Items in a menu are either a "Section" or an "Option". Both are links, but a Section can be expanded (or start out expanded, ideally, though my site has a problem with that).

2) Trees of classification can be done with the "Categories" option. Editing categories is an option within the admin section. One item can be in multiple categories, which I find useful.
So - I can have a forum, I.e., "Dolphins", in two categories:

Animals
Mammals