Was hoping that this would be using the original UNIX typesetting tools like troff. Also, surprised to see that asciidoc wasn't deployed over markdown.
Emacs Org-mode is also supported on GitHub and can be integrated into some pretty fancy workflows involving inline LaTeX rendered in Emacs. Org-Babel allows for a “notebook”-esque interface with embedded code samples, which show up non-interactively on GitHub.
I don't understand how these links indicate that markdown development has stalled.
All these issues were only created recently, by one person, and are actually not in the right place for the type of discussion they're trying to prompt. CommonMark have a separate [forum](http://talk.commonmark.org/) for feature discussion, which seems quite active.
Looking at https://spec.commonmark.org/ , it does seem it has stalled. They'll need to put in another gear if they're ever going to reach 1.0 (if that's a goal..?).