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In my opinion, Fletcher Penney's MultiMarkdown (http://fletcherpenney.net/multimarkdown/) is the most complete, and reliable, parser for extended Markdown in existence. Right now it is being rewritten in C, making it possible to write a Ruby wrapper and then use it with Jekyll.
I've never been fond of Maruku, and Discount lacks a few features, such as footnotes. Please consider adding MultiMarkdown to Jekyll.
MultiMarkdown in Jekyll would be fantastic.
I have modified rtomayko's ruby markdown extension rpeg-markdown, which uses jgm's peg-markdown as a backend, to use fletcher's peg-multimarkdown mentioned by the OP instead.
I have imaginatively called it rpeg-multimarkdown, and you can find it at http://github.com/djungelvral/rpeg-multimarkdown. I haven't extensively tested it yet, but it works well for my needs.
Perhaps this brings multimarkdown and jekyll a bit closer together, although I don't know how much work would need to be done on jekyll to add another convertor.
Not too hard after all, thanks to the ability to drop new converters into jekyll. You can find a basic one here:
The trickiest part was finding a file extension that wasn't swallowed up by the markdown file extension regexp. I went for /multi/i, but I don't know what would be best in practice.
The trouble with using a converter plugin with a special extension is that it won't work at all on github pages. The alternative is to modify lib/jekyll/converters/markdown.rb, which requires forking Jekyll.
Ideally, drop-in converters would be allowed (via the priority setting?) to override the built-in converters for a given format. This would make adding one's favorite flavor of markdown (MMD, pandoc, or whatever) trivial, and since these plugins are ignored on github pages, you would have a reasonably graceful fallback there.
I'd also much rather use multimarkdown headers than an unholy blend of YAML and Markdown for my postings.
Does anyone know if the rpeg-multimarkdown implementation allows any arbitrary code execution (possibly via LaTeX support, etc)? I'm happy to merge #379 if I can be convinced it will be safe for use by GitHub Pages.
Without assurance that no arbitrary code can be executed, I'm going to close this. Re-open if we can ensure that arbitrary code execution isn't a problem.