neo_doxygen: Fix the handling of the inner classes and of the root namespace

* Make the generation of the implicit modules more robust. Do not try to guess the namespace of the classes. Instead, wait to receive enough of explicit information to make a decision. This permits to list class in the root namespace and inner classes in the good module.
* List classes in the root namespace.
* Enhance the presentation of the inner classes so Nitdoc list them as part of their outer class.

Signed-off-by: Jean-Christophe Beaupré <jcbrinfo@users.noreply.github.com>


To make it consistent with the conditions with `has`.