I developed my Markdown editor, KeenWrite[0], to replace the shell scripts described in the Typesetting Markdown series[1]. KeenWrite takes in YAML document metadata (for variables), (R) Markdown documents, and generates XHTML. The XHTML is passed to ConTeXt[2] for PDF typesetting.
A feature matrix[3] compares various text formats and ecosystems for generating PDF files.