In order to remove warnings about /apidoc/*.rst files being included
multiple times in toc when building full swh documentation, prefer to
include module indices only when building standalone package documentation.

Also include them the proper sphinx way.

Related to T4496

This is the second part of 240ae09d.

Related to T4228

this is far from completion.

When building the global swh documentation, all commands defined
in other swh packages will be insterted in the swh.core cli
documentation but we only want to document the root command here.

This also fixes the remaining sphinx warning when building the global
swh documentation.

Related to T2265

related to T1330

change cherry picked from python module template
commit 71b117ba0cf9f1251b1cac26d0994df03a4c787d