A custom preprocessor for Marked 2 that will export two files after Marked does initial inclusion and processing, then cancel the processor and have Marked resume processing.

marked_lyx.sh

#!/bin/bash

# A custom preprocessor for Marked 2 that will export two files after Marked
# does initial inclusion and processing, then cancel the processor and have
# Marked resume processing.

# Install the latest version of MultiMarkdown:
# http://fletcherpenney.net/multimarkdown/download/

function main()
{
	# MARKED_PATH contains the full path to the document opened in Marked
	local filepath=$MARKED_PATH

	local dir=`dirname $filepath`
	local filename=`basename $filepath .$MARKED_EXT`

	# create a compiled version of the Markdown in the same folder as the
	# original document
	cat > $dir/$filename-compiled.md

	# create a lyx version in the same folder as the original document
	/usr/local/bin/multimarkdown -t lyx $dir/$filename-compiled.md > $dir/$filename.lyx

	# Returning "NOCUSTOM" tells Marked to skip the processor and resume rendering
	echo "NOCUSTOM"
}

cat | main $@