I am adding citation support that doesn’t rely on Pandoc to Weave.jl Add support for citations by mpastell · Pull Request #185 · JunoLab/Weave.jl · GitHub.
I have extended Julia Markdown to parse citations from text and using Update for Julia 1.x by mpastell · Pull Request #1 · JuliaTeX/BibTeX.jl · GitHub to parse bibtex.
The current state is that Latex output works, html works apart from formatting the references. If BibTeXFormat.jl get’s updated then it would be easy to get nice html output as well.