Fix and clean up documentation

[rly]

This PR:

• fixes docs makefile for Windows
• updates conf.fy to remove deprecated code
• makes the docs refer to Python 3.8 instead of 3.5
• adds missing packages to the api_docs page
• fixes all Sphinx warnings

The sphinx docs should now build and validate successfully, without warnings.

[codecov]

Codecov Report

Merging #260 into dev will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev     #260   +/-   ##
=======================================
  Coverage   70.31%   70.31%           
=======================================
  Files          33       33           
  Lines        5935     5935           
  Branches     1394     1394           
=======================================
  Hits         4173     4173           
  Misses       1327     1327           
  Partials      435      435

Impacted Files	Coverage Δ
src/hdmf/data_utils.py	90.07% <ø> (ø)	⬆️
src/hdmf/spec/catalog.py	92.07% <ø> (ø)	⬆️
src/hdmf/backends/hdf5/h5_utils.py	62.69% <ø> (ø)	⬆️
src/hdmf/utils.py	92.21% <ø> (ø)	⬆️

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