Clean up the RST doctree.

[eirrgang]

This change addresses several issues:

• Several docs are included multiple times.
• Several autodoc directives are duplicated.
• Subpackages do not have effective base module documentation targets.

To deduplicate documentation, the doctree is simply flattened a bit, though section delimiters are adjusted to better represent the document hierarchy.

Since there is no docstring for most packages (__index__.py files), the automodule directive didn't do anything, and is replaced with a static module directive in the rst document.

Ref #375

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 61.46%. Comparing base (d624ce1) to head (747e953). Report is 312 commits behind head on devel.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #376 +/- ## ======================================= Coverage 61.46% 61.46% ======================================= Files 60 60 Lines 6721 6721 ======================================= Hits 4131 4131 Misses 2590 2590 ```

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