I don't know how to even boil the problem down to specific questions. A fish is swimming happily along, and suddenly finds itself within an object. Well, it's already too late - there has been a collision. But even then, how to get out of the predicament? Does it back up? What if there is now another fish behind it? And a fish behind that one?
At the moment, I'm using a terrain-height map to watch for collisions with the environment, but this scheme is fairly easy to fool, expecially if a fish is travelling back-to-front.
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