♻️📚 Restructure code base and documentation

[chrisjsewell]

This PR restructures the code base into modules, to be more coherent as to the purpose of each module.

It also restructures the documentation, to make it easier for users to follow, and expose the core concerns at the top-level.

Finally, it introduces document-level configuration via the Markdown top-matter, under the myst key.
This configuration is generated from the code MdParserConfig dataclass, so is inherently consistent with global configuration.
The (YAML) top-matter of a MyST file is always read (within the docutils/sphinx parsers) before the full document is parsed, in order to acquire this file configuration, which overrides the default/global configuration (see docs/configuration.md).

Breaking changes

This should not be breaking, for general users of the sphinx extension,
but will be for anyone directly using the Python API, mainly just requiring changes in import module paths.

The to_docutils, to_html, to_tokens (from myst_parser/main.py) and mock_sphinx_env/parse (from myst_parser.sphinx_renderer.py) functions have been removed.
These were really just for testing, and were confusing for users, since they did not run the full sphinx build.
Instead, for single page builds, users should use the recently added docutils parser API/CLI (see docs/docutils.md),
and for testing, functionality has been moved to https://github.com/chrisjsewell/sphinx-pytest.

The top-level html_meta and substitutions top-matter keys have also been deprecated (i.e. they will still work but will emit a warning), as they now form part of the myst config, e.g.

---
html_meta:
  "description lang=en": "metadata description"
substitutions:
  key1: I'm a **substitution**
---

is replaced by:

---
myst:
  html_meta:
    "description lang=en": "metadata description"
  substitutions:
    key1: I'm a **substitution**
---

[codecov]

Codecov Report

Merging #566 (0676b68) into master (7dda7b5) will increase coverage by 0.19%.
The diff coverage is 88.61%.

@@            Coverage Diff             @@
##           master     #566      +/-   ##
==========================================
+ Coverage   89.64%   89.83%   +0.19%     
==========================================
  Files          17       20       +3     
  Lines        2154     2116      -38     
==========================================
- Hits         1931     1901      -30     
+ Misses        223      215       -8     

Flag	Coverage Δ
pytests	89.83% <88.61%> (+0.19%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
myst_parser/mdit_to_docutils/utils.py	81.81% <ø> (ø)
myst_parser/mocking.py	87.05% <71.42%> (+0.83%)	⬆️
myst_parser/mdit_to_docutils/html_to_nodes.py	90.74% <80.00%> (ø)
myst_parser/parsers/docutils_.py	81.08% <81.08%> (ø)
myst_parser/config/dc_validators.py	85.45% <82.75%> (ø)
myst_parser/config/main.py	86.91% <86.91%> (ø)
myst_parser/sphinx_ext/main.py	90.62% <90.62%> (ø)
myst_parser/mdit_to_docutils/base.py	92.26% <91.30%> (ø)
myst_parser/mdit_to_docutils/sphinx_.py	94.17% <92.30%> (ø)
myst_parser/parsers/mdit.py	96.72% <96.72%> (ø)
... and 14 more

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