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I've set up individual cells for them with beds, workstations, food and water, it's been a couple days but they're still in the "Calm" status. They're also not equipping their class-specific equipment, even though there is enough of each item in storage.

Am I missing something? How long does the assimilation process take?

PS: I have a human settlement and my prisoners are human, a green bug-face dude and a cat guy.

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The 'happiness' part of the game is a bit underdeveloped and needs some work, but you should be able to make them happy with a Tavern, or by giving them some alcoholic drinks.

Also, sorry for such a late response!