Ugly, proof of concept filter to create section refs.

section-refs.lua

dkjson = require 'dkjson'
List = require 'pandoc.List'
utils = require 'pandoc.utils'

CitationOrig = pandoc.Citation

-- monkey-patch citation creation
pandoc.Citation = function(id, mode, prefix, suffix, note_num, hash)
  local res = CitationOrig(id, mode, prefix, suffix, note_num, hash)
  setmetatable(
    res,
    {
      __tojson = function (x)
        local tmp = {}
        for k, v in pairs(x) do tmp[k] = v end
        tmp.citationMode = {t = x.citationMode}
        return dkjson.encode(tmp)
      end
    }
  )
  return res
end

-- hacky, ad-hoc JSON conversion. Will fail for MetaString and MetaBoolean
function tojson(el) return dkjson.encode{t = el.t, c = el.c} end
for _, const in pairs(pandoc.Inline.constructor) do const.__tojson = tojson end
for _, const in pairs(pandoc.Block.constructor) do const.__tojson = tojson end
for _, const in pairs(pandoc.MetaValue.constructor) do
  const.__tojson = function (el)
    local tmp = el
    local mt = getmetatable(el)
    return dkjson.encode{t = el.t, c = setmetatable(tmp, {})}, setmetatable(el, mt)
  end
end

function flatten (lst)
  local res = List:new{}
  for i, el in ipairs(lst) do
    if el.t == 'Sec' then
      res[#res + 1] = pandoc.Header(el.level, el.label, el.attr)
      res:extend(flatten(el.contents))
    else
      res[#res + 1] = el
    end
  end
  return res
end

function Pandoc (doc)
  local res = List:new{}
  local sections = utils.hierarchicalize(doc.blocks)
  for _, sec in ipairs(sections) do
    local section_doc = pandoc.Pandoc(flatten({sec}), doc.meta)
    local section_json = dkjson.encode(section_doc)
    local filtered = pandoc.pipe('pandoc-citeproc', {}, section_json)
    res:extend(pandoc.read(filtered, 'json').blocks)
  end
  return pandoc.Pandoc(res, doc.meta)
end