Fix plutus-metatheory-site nix build script.

[Ramsay Taylor]

The command nix build .#plutus-metatheory-site should convert all the Literate Agda into HTML. There is a script in nix/plutus-metatheory-site.nix that partly works but I have a few problems:

1. It caches the Agda phase, which sounds good but it doesn't appear to re-run when I edit one or two of the Agda files. This might not be an issue for most people who don't want to re-run Agda every time they rebuild everything, but in my case I am editing the Agda and need to see the changes in a live, hyperlinked document
2. The jekyll command doesn't seem to index all of the files. The index works and many of the links from there work, but I have found several modules that seem to exist as .md but they don't get converted to html. I'm not sure if jekyll is only descending one level, or if it is based of a list somewhere? Scoped is an example - it is linked from index.html but doesn't get built.

[zeme-wana]

Addressed by #5959