GitHub provides Markdown-powered wikis. (At least, configurably
Markdown-powered.)

As far as automated conversion into other formats, including .doc
(shudder!), take a look at the much-respected Pandoc project. 

Also, be warned: Github Flavored Markdown (GFM) differs from Gruber's
original Markdown in a number of ways (and even more so when [[wiki
syntax]] is added). You may want to let Github provide the HTML output,
and pipe *that* into pandoc (modulo additional processing) for the best
and most reliable results.

Best of luck with your project!

Alan Hogan
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