Add mdformat to pre-commit config

[melissawm]

References and relevant issues

Closes #821

Description

This PR lints the entire repo. I am using mdformat with myst, and there are some limitations and caveats:

• Colon fence syntax is not currently supported by the linter. I have tried to separate out these changes in a specific commit so they're easy to revert if we want to (see colon fence syntax is broken by escape character executablebooks/mdformat-myst#13 for context)
• There are some escapes enforced here (like \[) that we don't really need but I guess they don't hurt and the benefit in the end is a net positive (having the linter turned on by default)
• I have excluded the naps folder from the linter because the rst syntax for the file metadata creates issues. We can explore if we want to touch those in the future but I don't think they are critical to lint.

Most of the motivation for this is to catch syntax issues early before a contributor actually submits a PR or has to build the docs locally.

Run mdformat with pre-commit. This is a test to see how the formatter behaves.

[psobolewskiPhD]

Just for my sanity: you first converted all the colon fencing manually or using another tool, and then the normal mdformat was able to work basically?

[melissawm]

Yes, exactly!