I would think that the alliances are ways clans of three can join up for six player Raids. I have searched around the web for a better explanation but haven't found one. Ideally having two clans w/ 3 players joining together in a raid would be easier than patrolling msg boards looking for more members. Haven't gotten a chance to test out the Raid, so all this is in theory.
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Thanks for answering, that makes a lot of sense! :)