When a world loads (or is saved?) then the biome assignment should be checked against any influence that the player has had on the world and update it accordingly:
If a player chops down all the trees in a forest, it should now be a planes. If they build a mountain it should be mountains. If they sink a bit hole and fill it with water it should be an ocean. If they plant loads of jungle trees it should become a jungle. If they turn the landscape into a sandscape it becomes a desert... etc.
This would mean that specific biome mobs have a chance to spawn and the weather would change. And the biome specific colour deviation would be applied.
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