bavbavhaus.net/pandoc/collect_notes.lua

local read = pandoc.read

assert(#arg == 1, "\n" ..
  "[ERROR] usage: pandoc lua collect_all.lua <index file>")

local visited = {}
local function collect (fp)
  local f = assert(io.open(fp), "\n" ..
    "[ERROR] could not open " .. fp .. " for reading.")
  visited[fp] = true
  io.write(fp .. "\n")
  local data = f:read("a")
  f:close()
  read(data):walk({ Link = function (link)
    if not link.target:find(".%.md$") then return end
    local f = io.open(link.target)
    if f == nil then return else f:close() end
    if visited[link.target] then return end
    visited[link.target] = true
    collect(link.target)
  end })
end

collect(arg[1])