Created attachment 195841 [details]
Example exhibiting the bug

If an external module contains external submodules, the module listing does not display the nesting.

The attached example illustrates what I mean. There are four files:

   doc/Doxyfile-main
   doc/Doxyfile-unsupported
   src/modules.c
   unsupported/src/unsupported-modules.c

Doxyfile-main generates the documentation for src/modules.c which contains two modules, 'Module A' and 'Module B'. 

Doxyfile-unsupported generates the documentation for unsupported/src/unsupported-modules.c which contain one module called 'Unsupported modules'. That module contains two submodules, 'Module U1' and 'Module U2'.

Both sets of documentation exchange information via tag files.

The module list generated by Doxyfile-unsupported is as expected:

   * Unsupported modules
       * Module U1
       * Module U2
   * Module A [external]
   * Module B [external]

However, the module list generated by Doxyfile-main is NOT as expected:

   * Module A 
   * Module B
   * Unsupported modules [external]
   * Module U1 [external]
   * Module U2 [external]

It does not indicate that 'Module U1' and 'Module U2' are submodules of 'Unsupported modules'. I would like to say this:

   * Module A 
   * Module B
   * Unsupported modules [external]
       * Module U1 [external]
       * Module U2 [external]

This looks similar to bug 172964, but that is a very old report, and it also states that tag files do not store group membership, while it seems to me that they do indicate group membership but that it is not used when generating the module list.