Refactor the extension to use a Sphinx Domain

[mikemckiernan]

• Add optional command index and optional commands-by-group index.
• Optionally, print fully-qualified subcommand name in title.
• Support commands:command role for intersphinx.
• Prefer fully-qualified HREF targets:
  • Use targets like "#blah-sub-commands" as the primary target and move historic targets like "#Sub-commands" to secondary targets.
  • Preserve the older HREF, "#sub-commands", as a secondary target. In the HTML, this becomes a span just below the section element so that bookmarks continue to work even after adopting the update from this commit.