I wrote a small wrapper to include dokuwiki-Markup for github Readme files.
I've chosen the extensions .doku and .dokuwiki for that. You have to get a current version of dokuwiki (available at http://www.splitbrain.org/projects/dokuwiki) and extract it somewhere the script can access it (I've put it beneath the lib/github/commands). I didn't include it into the commit.
The script simply wraps Dokuwiki's bin/render.php-tool to render text into HTML.
The commit is available here:
I couldn't run the tests, though. All tests (not just Dokuwiki) failed. But the test SHOULD work. Perhaps somebody with more ruby-knowledge could test it somewhere.