This is my gist.

pandoc-filter.js

/*** 
Can take generated HTML export from PubPub and convert to other formats with proper footnotes and citations

Requires pandoc (probably from brew), pandoc-filter from NPM

pandoc -s <source.html> -f html -t <format> -o <otput.format> --filter ./pubpub-filter.js 
***/

const pandoc = require('pandoc-filter');
const Cite = pandoc.Cite;
const Str = pandoc.Str;
const Div = pandoc.Div;
const Note = pandoc.Note;
const Plain = pandoc.Plain;
const Para = pandoc.Para;
const RawBlock = pandoc.RawBlock;
const Span = pandoc.Span;

function action(type,value,format,meta) {
	if (type === 'Div' || type === 'Span') {
		const [[ids, classes, kvs], contents] = value;

		if(classes.includes('citation-wrapper') || classes.includes('footnote-wrapper')) {
			console.error('\ncontents in:\n', JSON.stringify(contents), '\n');

			/* all inline */
			//const new_contents = Span(["",[],[]],[Note([Plain(contents)])]);

			/* all block */
			const new_contents = Plain([Note(contents)]);

			/* block --> inline */
			/* not functioning in all cases? */
			//const new_contents = [Plain([Span(["",[],[]],[Note(contents)])])];


			console.error('\ncontents out:\n',JSON.stringify(new_contents),'\n');
			return new_contents;
		}

		if(classes.includes('count-wrapper')) { return [] };

		//if(classes.includes('render-wrapper')) { /* convert to inline? */ }

	}
}

pandoc.stdio(action);