pandoc --pdf-engine=latexmk --natbib --bibliography=bibliography.bib --input=test.md --output=test.pdf

If I have a markdown file like this, I expect all the citations in bibliography.bib to be in the PDF:

---nocite: |  @*---

I think that the problem is that the code to add\nocite to the template, first addedhere, puts it in the preamble, not the body. That's fine for biblatex but not bibtex.

This seems like an easy fix: moving the code to the body. That would mean removing it from the common.latex partial and adding it to both the default.latex and default.beamer partials.

One concern is that the current situation works with biblatex and there might have been a reason for having the nocites in the preamble. Biblatex is happy with them in the body but I think it can change the order of references in some cases.