In one project, some pages were added - it was a new project in which doxygen was being tested properly - adding comments & pages - rather than simply auto-generating docs from our existing code-base.

The problem is when doxygen is run on the main code-base, that project's pages show up at a top level. e.g they have a main-page and some sub-pages. But what we'd want is all those pages pushed down one level so you have main->project-main->project-pages.

One question is what happens if multiple projects have a main-page? Do they get combined, or throw errors?

Another question is if you can tell doxygen to use paths and containing folders to auto-generate groups or sections or page-hierarchies in some way? Going through all out projects to properly assign classes to groups is a mammoth task, so ideally everything in a directory would get put in a group of that name, as a way to make the documentation of non-doxygen codebases better.

Sorry my question is a bit vague, the problem is even after reading the docs the terminology isn't totally clear yet. Hopefully the kind of question I'm asking is clear, if not I'll try to cobble an example file-structure together.