I store Markdown code in MySQL, and I’m worried about how to convert it back to HTML without transferring it through the WMD control and using massive data transfer.
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I think there is a misunderstanding — the WMD control does Markdown to HTML conversion on the client web browser, in JavaScript.
But the Markdown text is no longer on the client — it is on your server, in your MySQL database. Thus, you need a Markdown library that runs on your server.
Try checking the Markdown wiki page there are dozens of server Markdown libraries there.
http://xbeta.org/wiki/show/Markdown
Pick one, put it on your server, and run it on your server to convert the Markdown in your database to HTML.