Black Mesa provides a standalone installer that extracts the game to the Steam folder, so Steam can manage launching the game as well as providing the Steam Overlay in-game.
However, Steam doesn't manage uninstalling the game as it wasn't installed through Steam (the game has been Greenlit
but it's not yet available in the store as of Sep 2012 and is now available for download via Steam). How do I completely uninstall Black Mesa in this case? It seems I can just remove the
steamapps/SourceMods/BMS folder and the shortcut from
steam/games, then restart Steam, but I'm not sure if that covers it entirely.