fix examples for ref and autoref

[sneakers-the-rat]

Fix: https://github.com/openjournals/joss/issues/1340

looks like this wasn't working even before the transition to myst: https://web.archive.org/web/20230925202053/https://joss.readthedocs.io/en/latest/submitting.html#internal-references

left in the mention of the markdown-style labels even if they aren't working for now bc i assume that will be fixed.

Before:

After:

[xuanxu]

@arfon about ConTeXt vs LaTeX: any word on what you think we'll use in the future?

[sneakers-the-rat]

Gotcha! Didnt know that. Feel free to close this if other plans