Mentioning the limitations of YAML files in the docs

[john-science]

What is the change?

This is a small change to the docs where I explicitly mention the "duplicate keys" limitation of YAML files.

Also, and I'm sorry about this, I did a tiny bit of cleanup in the docs; mostly whitespace.

Why is the change being made?

After much trial-and-error, it doesn't appear reasonable that we will build our own YAML reader to close #433.

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Checklist

• This PR has only one purpose or idea.
• Tests have been added/updated to verify any new/changed code.

• The code style follows good practices.
• The commit message(s) follow good practices.

• The release notes have been updated if necessary.
• The documentation is still up-to-date in the doc folder.
• The dependencies are still up-to-date in pyproject.toml.

[john-science]

Bump