Those are generally used a like GET variables, it's just a way of passing information along with your request. There are a few different ways to implement this but the aim is usually to have cleaner looking urls. I'm confused why they left the index.php in there - it could be a poorly done homebrew attempt. (Not that I have anything against homebrew solutions for common problems - best way to learn IMO)
If you want to figure out more, look for instances in the code where information is needed about which article to pull, etc... See where that information is coming from and work backwards. If you can't figure out how it works from the code then go through .htaccess and look for url rewriting logic.