Thanks for the quick reply! I will look into adding the correct cite-proc add-on.
If possible, could you explain why bookdown can't just point to it's own pandoc installation and ignore the global pandoc path every time it is run?
There is an explanation confirming the limitation here, but no details as to why bookdown can't just look for the one it was installed with.
Good question. Unfortunately the answer is "no". Ideally we should allow users to choose a specific version of Pandoc in rmarkdown, but currently rmarkdown only looks for the highest version of Pandoc in your system.
I think my solution is most likely to uninstall the version of pandoc I added earlier (I can't remember why I did that in the first place).
Edit: Ah I see. this choice was actually to make it less dependent on Rstudio. I didn't realize that the pandoc download was Rstudio's doing, not Bookdown's. I am not familiar with the limitations R has with downloading executables, but it would be great if bookdown could check for pandoc compatibility and download missing elements as needed on its own. So if it sees a newer version of pandoc, to add the citeproc add-on. But that could turn into a dependency mess. These are hard problems!
EDIT: it turns out my miniconda installation also installed pandoc! Who knows how many pandocs I actually have on my computer. Maybe the solution is for pandoc to start bundling citations with its executable
PS: To anyone saying that you should keep a bibtex file with markdown notes stored in the comment field, don't! Bibtex and jabref delete line breaks when they open or edit .bib files. So all the markdown formatting will go out the window if someone else decides to even open the file you've worked on.