Filter to include Markdown files via code blocks

include.lua

--- Pandoc Lua filter to include other Markdown files
---
--- Usage: Use a special code block with class `include` to
--- include Markdown files. Each code line is treated as the
--- filename of a Markdown file, parsed as Markdown, and
--- included. Metadata from include files is discarded.
---
--- Example:
---
---     ``` {.include}
---     chapters/introduction.md
---     chapters/methods.md
---     chapters/results.md
---     chapters/discussion.md
---     ```
local List = require 'pandoc.List'

function CodeBlock(cb)
  if cb.classes:includes 'include' then
    local blocks = List:new()
    for line in cb.text:gmatch('[^\n]+') do
      if line:sub(1,1) ~= '#' then
        local fh = io.open(line)
        blocks:extend(pandoc.read (fh:read '*a').blocks)
        fh:close()
      end
    end
    return blocks
  end
end

Concluding this dialog for posterity, @tarleb and I conversed offline and he came up with a modification to his lua plugin, and a couple more lua plugins.

include.lua

--- Pandoc Lua filter to include other Markdown files
---
--- Usage: Use a special code block with class `include` to
--- include Markdown files. Each code line is treated as the
--- filename of a Markdown file, parsed as Markdown, and
--- included. Metadata from include files is discarded.
---
--- Example:
---
---     ``` {.include}
---     chapters/introduction.md
---     chapters/methods.md
---     chapters/results.md
---     chapters/discussion.md
---     ```

local List = require 'pandoc.List'

function CodeBlock(cb)
  if cb.classes:includes'include' then
    local blocks = List:new()
    for line in cb.text:gmatch('[^\n]+') do
      if line:sub(1,1)~='#' then
        local fh = io.open(line)
        blocks:extend(pandoc.read (fh:read '*a').blocks)
        fh:close()
      end
    end
    return blocks
  end
end

delink.lua

delink.lua is shorter and faster than delink.hs, and doesn't require Haskell to be installed.

function Link (link)
  return link.content
end

no-includes.lua

This no-includes.lua filter removes all include blocks. The filter is used when targeting man output.
Using include.lua would also work, but this filter is faster.

function CodeBlock (cb)
  if cb.classes:includes 'include' then
    return {}
  end
end

I also updated my bash script to use the plugins:

#!/bin/bash

function pandocHtml {
  # Reads Pandoc markdown version, writes man page
  # $1 - filename, including file type, which should be .md
  # $2 - uncompressed output filename, with file type
  sudo bash -c "pandoc $1 -s \
    --lua-filter=scripts/include.lua \
    --lua-filter=scripts/links-to-html.lua \
    --css=http://cadenza.micronauticsresearch.com/css/main.css \
    --css=http://cadenza.micronauticsresearch.com/css/man.css \
    --from markdown \
    --to html > \"$2\""
}

function pandocMan {
  # Reads Pandoc markdown version, writes man page
  # $1 - filename, including file type, which should be .md
  # $2 - uncompressed output filename, with file type

  sudo bash -c "pandoc $1 -s \
    --filter scripts/delink.hs \
    --from markdown \
    --to man > \"$2\""
}

# Make the script directory current
cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1

pandocHtml cad.md cad.html
pandocMan  cad.md cad.1.man

This is a very nice little filter -- thanks!