Clean up Sphinx warnings related to models

[jessica-mitchell]

This PR resolves some of the warnings that Sphinx outputs related to models.

Many of the changes are related to items in the bibliography that were not cited properly.
There are also syntax fixes.

Because the restructured text files for models are autogenerated from a script, Sphinx warns that it doesnt' have them indexed.
So this PR also indexes the files by creating a JSON file from the extractor_userdocs.py that Sphinx reads and outputs in Jinja templated table of contents.

Fixes #1907

[terhorstd]

Amazingly many details fixed! Thanks a lot!
Some double-backtics need a look, as discussed.

[jessica-mitchell]

@terhorstd I addressed your comments, but since this was updating the double back ticks for some of the terms, I decided to go through and try find all terms that needed double back ticks and add them.

[terhorstd]

This really fixes a lot of broken documentation! Much appreciated!!!
🚀

I have some small questions and comments just for clarification. Of course there are still tonnes of unquoted variables or math terms around, enough for such PRs in months to come. For this one we should however not take more changes into the set. Let's try to finish this one first, then eventually start a new one.

[heplesser]

I just tried to build documentation from this branch. This failed because nest could not be imported with our fancy new way of managing the nest module in Python. Has anyone else seen this problem? The testsuite runs find and PyNEST works otherwise.

Running Sphinx v3.5.3

Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/Users/plesser/miniforge3/envs/nest-simulator-dev/lib/python3.9/site-packages/sphinx/config.py", line 327, in eval_config_file
    execfile_(filename, namespace)
  File "/Users/plesser/miniforge3/envs/nest-simulator-dev/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 88, in execfile_
    exec(code, _globals)
  File "/Users/plesser/NEST/bld_jessica/doc/userdoc/conf.py", line 87, in <module>
    nest.NestModule = type(nest)
  File "/Users/plesser/NEST/src/pynest/nest/__init__.py", line 423, in _setattr_error
    raise err from None
AttributeError: can't set attribute 'NestModule' on module 'nest'

[jougs]

Many thanks! This is really a great improvement. Above my suggestions, I have a feeling that there might be more variable names in the tsodyks_* files that need marking up.

[jougs]

@heplesser: This should be fixed by #2244.
@jessica-mitchell: can you please merge upstream/master?

[jougs]

And just for the record: There is a certain potential for conflict with #2246.

[jougs]

@jessica-mitchell: friendly ping!

[jessica-mitchell]

@jougs thanks for the reminder -I am working on this - Sphinx failed to build after the changes you or Dennis made in the extractor_userdocs.py were committed, so I'm trying to fix it (I have a fix, but I've noticed another issue, which I'm looking into)

[jougs]

The recent commits address all my concerns. Thanks again!

[terhorstd]

Lots of improvements! Thanks for making the docs a better place! 👍