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 T4496

docs/index.rst

@@ -11,4 +11,12 @@
    configuration
    Design notes <design>
    Tutorial <tutorial>
-   API reference </apidoc/swh.fuse>
+
+.. only:: package_doc
+
+   Indices and tables
+   ------------------
+
+   * :ref:`genindex`
+   * :ref:`modindex`
+   * :ref:`search`