It doesn't make much difference for the food, but with the water, I'd say keep it inside, if you have a concrete flooring, but otherwise, leave it outside as much as possible to avoid a rotting floor. Our old coop was raised, and had a wooden floor, and within five years, the floor rotted, and fell through, but now, in our new coop, we have a cement floor, and keep the food and water inside all day.
I am seriously thinking about putting vinyl floor in mine. Does anyone have any experience with how much longer it will make the floor last?