I'm using doxygen to generate an API reference from source code, aiming to convert it into a CHM help file and eventually into a plugin for Eclipse. Unfortunately the default ordering and nesting of the classes, namespaces, etc. in the Table of Contents is not exactly ideal and I'd prefer to customize it if possible.

By default, doxygen creates two indexes/menus for navigating the generated documentation. One is the common Table of Contents on the left frame and the other is the row of buttons at the top of each individual HTML page. The latter can be comfortably customized by editing the layout xml file as described in doxygen manual (see section 'Changing the layout of pages') but so far I've seen no way to do similar modifications for the Table of Contents.

To use a precise example, I'm looking for a way to nest the three standard topics Class List, Class Hierarchy, and Class Members as subtopics inside a parent topic in the TOC, as is done by default in the menu system that's located on top of every page.

I'd imagine this is not the most unusual issue and may have a known solution available.

Thanks for your assistance!