Yeah, I've been expecting someone to work up a system where:
- source file is .md
- file is compiled to .pdf _and_ the .md source file is included as an attachment
- when working with the file beyond viewing as a .pdf the .md is extracted and used instead of the .pdf
The LaTeX folks have a similar system ages ago where the .tex source would be included in a .pdf made from a .tex file for embedding in documents so that it could be sent in say an e-mail and then edited by the recipient --- absolutely awesome for discussing math via e-mail.
That's a good concept but I don't think Markdown is expressive enough for all the layouts & formatting that people typically want in PDFs. More likely that the source format would be something like HTML or SVG or .docx.
Restructured text has mostly 1:1 correspondence with Docbook. I use an XSLT transform to convert its XML schema into Docbook and PDF from there via XSL-FO.