docs: Include module indices only when building standalone package doc
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 swh-docs#4496 (closed)
Depends on swh-docs!271 (closed)
Test Plan
Once that diff validated, I will push similar commits for all swh packages.
Migrated from D8951 (view on Phabricator)