Propagate code citations into user manual

[sethrj]

This (re)defines doxygen commands \cite, \citet, and \citep for adding citations as a combination of Zotero keys and DOI URLs (or just other URLs). The procedure to add references is:

1. Add the reference to the appropriate subdirectory of the Zotero Celeritas References subgroup. (Contact @tmdelellis if you are not a member of the group.) If you have a DOI there's a handy magic wand icon "Add items by identifier".
2. In the Extra field, add a special line Citation key: author-keyword-year to set up a stable BibTeX citation key. (see https://github.com/retorquere/zotero-better-bibtex for how this works).
3. For now ask Seth to update the zotero .bib file that lives at https://github.com/celeritas-project/celeritas/tree/doc/gh-pages-base . TODO: this is necessary before the pull request passes! I should add a github action to update the bibliography file.
4. Subsequent Github action builds should pull in the new bib file for generating documentation. For your local build you may have to remove the source/doc/_static/zotero.bib so that CMake will re-download it.

[github-actions]

Test summary

 1 924 files   3 039 suites   1m 9s ⏱️
 1 343 tests  1 308 ✅ 35 💤 0 ❌
10 261 runs  10 233 ✅ 28 💤 0 ❌

Results for commit f6e2e0a.

[amandalund]

Should we include the instructions on how to add references to the zotero group and update the bib file?

Suggested change

	referenced inline code using the special ``\citep{whatever-2025,
	referenced inline code using the special ``\citep{author-keyword-year,

[sethrj]

Absolutely; and it turns out I neglected to push that commit 🙃

[amandalund]

Are most of these not in the bib file yet? I get some warnings about bibtex keys not found.

[sethrj]

Yeah, this is blocked on some changes in the main docs that I put into #1562 from which this PR was split out.

[amandalund]

Now I'm only seeing a single entry in the references (the PRM), I guess because it's the only one that's currently both in the bib file and being cited? Will we need to go through and update the other citations in the docs if we want them to appear here?

[sethrj]

Yes, or we could manually use the :cite:empty: directive to force inclusion of some.

What I'd like to do is export a bibliography set if and only if the zotero entries have a "citation key": i.e., we want to cite it in a work. And then to automate that export process.