Pandoc multiple files
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The only additional tweaks necessary to get citation support were calling it with the '--filter pandoc-citeproc' arguments, which lets it process any bibliography data supplied in the header metadata for the files. Calling Pandoc with --bibliography <path to bibliography> (as in my example above) is a shortcut for calling it with --metadata ...
You can create your output (in the form of pdf, html, latex or even docx) from md using pandoc with a simple command then: pandoc input.md --bibliography=mybib.bib -o output.pdf Note: In case you need it, you can see the citation key values of your items in Zotero Info pane (these values are auto-generated by Better Bib(La)TeX for Zotero ):