Read about how the AI works at my blog.
Yes, there are three main classes. The one in 'BaseAQAGame' is the main start which is used if you want to play a game against the AI. The one in 'AI' is very similar to that in 'BaseAQAGame' but it will not display the board - this is used to assist the 'GeneticOptimiser' which will automatically generate optimal weightings for the AI.
Thanks to AQA for providing the original game code which is in the 'BaseAQAGame' section and has only been modified slightly by me.