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Note for those with MMD 5 questions or bugs
Rather than reply to everyone individually with the same thing, I'll use this for a "landing page" for those who write with bugs/suggestions/questions about MMD 5.
MMD 6 is close to being finished. As of 2017-02-11, HTML support has only a few features that are not available (see milestones for features remaining to complete HTML support). Once HTML is finished (in version 0.2a), then I will work on LaTeX support (this should be relatively easy, but might point out a few things that need to be fixed.) Once LaTeX is done in version 0.3a, it should be even easier to add support for other output formats (e.g. ODF, beamer, memoir, etc). At that point, MMD 6.0 should be ready
The parser in MMD 6 is completely different than that used in MMD 3/4/5. I'll write up more technical details sometime (see the README for some explanation), but some bug fixes will already be fixed by virtue of the new parser approach. For that reason, I will not put time into fixing those things in MMD 5. That time is better spent getting MMD 6 finished, which will fix many issues at once!
MMD 6 is useable for HTML already (minus the few features that aren't finished yet.) It is available in the Babelmark 2 web tool (thanks to John MacFarlane!). Feel free to download and compile MMD 6 yourself (it won't be available as a binary until v 6.0), or try it out on Babelmark 2. Do keep in mind, however, that the version used on Babelmark 2 may be a little behind what is available on github.