Madoko – Write full-blown academic articles in Markdown
You also might want to take a look at GitBook (https://www.gitbook.com/).It supports both Markdown and AsciiDoc and is used by authors to write books, documentation, research-papers (GitBook has great TeX support, in all outputs: web, pdf, epub, mobi). (Here's a math heavy book for example: http://jandeleeuw.gitbooks.io/bras1/content/blockrelaxation/...)The format and toolchain itself is open-source (https://github.com/GitbookIO/gitbook)There's a ecosystem built on top of that such as a Desktop Editor (https://www.gitbook.com/editor), plugins (http://plugins.gitbook.com/), and more ...I don't want to hijack the current thread, Madoko seems really cool, I thought some of you might be interested in a more established solution. I'm happy to answer any questions !Disclaimer: I'm one of the GitBook co-founders