Modernise Sphinx configuration

This change brings the configuration closer with what the latest
sphinx-quickstart generates. It also makes it easier to read through the
documentation configuration file as well.

- Remove unset configuration options
- Drop configuration options that are set to their default values
- Remove placeholder comments, including inline documentation of options
- Group configuration options into sections with links to detailed docs
- Move all custom logic toward the end of the file

Author: pradyunsg