Excellent questions. Here are the rules pertaining to the tournament structure (from the readme):

One submission per person.

The tournament will be round-robin elimination: Each bot will play one match against all other bots, where a match consists of 100 rounds of the prisoner's dilemma. At the end of the round-robin round, the lower-scoring half of the tournament pool will be eliminated. This process will be repeated until only one bot remains, or there is a tie. The whole tournament will be run 1000 times, and the bot that places first most frequently will be declated the overall winner.

In other words, bots do not play against themselves, but they will play against all other bots at least once per tournament iteration. Let me know if this is unclear. (This setup was suggested to me by James Miller.)