Since we weren't autodoc'ing the modules during the docs build, the
module index link was broken.
This generates the module docs (but hides them from the main top-level
table of contents) so they can be accessed via the 'Module Index' link.
Also cleans up some docs issues so that warnerrors=True works during
sphinx-build.
Closes-Bug: #1472642
Change-Id: I5a3a16d1e81b12237452d5a3a3f7f0cc42618e88