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Supporting or switching to MultiMarkdown would take care of a few of the outstanding feature requests. Quoting from the MultiMarkdown site:

MultiMarkdown is a modification of John Gruber's original Markdown.pl file. It uses the same basic syntax, with several additions:

  1. I have added a basic metadata feature, to allow the inclusion of metadata within a document that can be used in different ways based on the output format.
  1. I have allowed the automatic use of cross-references within a Markdown document. For instance, you can easily jump to [the Introduction][Introduction].
  1. I have incorporated John's proposed syntax for footnotes. Since he has not determined the output format, I created my own. Mainly, I wanted to be able to add footnotes to the LaTeX output; I was less concerned with the XHTML formatting.
  1. Most importantly, however, I have changed the way that the processed output is created, so that it is quite simple to export Markdown syntax to a variety of outputs. By setting the Format metadata to complete, you generate a well-formed XHTML page. You can then use XSLT to convert to virtually any format you like.

MultiMarkdown would solve the BibTex request and the multiple output formats would make the print_link request an easy fix. MultiMarkdown is actively developed and can be found at:

MultiMarkdown Homepage

I don't think MultiMarkdown solves [[the BibTeX request|todo/BibTeX]], but it might solve the request for LaTeX output. --[[JoshTriplett]]