Currently, "md" is the only extension identifying markdown files for Doxia. There are many  extensions identifying markdown. GitHub uses "md", but it is also interpreting markdown somewhat differently . Wikipedia article  offers "markdown" as an alternative extension, citing  the author of markdown, who agrees  with proponents of this extension.
Please, add a support for "markdown" extension;
possibly keeping it for standard markdown and leaving "md" for the GitHub style.