For our notebook format at Nextjournal we use an edn appendix to store metadata like results and environment (docker image). The user-edited content is just plain markdown, while also being runnable reproducibly. See [1] and run it at [2].

[1]: https://github.com/nextjournal/notebook-format-demo/blob/mas...

[2]: https://github.nextjournal.com/nextjournal/notebook-format-d...