Ok so I built this barn three year years ago, with natural systems for animal waste as a priority!
So the whole barn sits on a hand squared barn stone ring that is on a gravel base. ( squared the stone myself with hand tools)
Then the barn can be built in timber, lumber or any method, mine was scrap lumber that I misered away for a while!
Then the whole barn is off the ground by 12-14" so the barn has a "hole"in it, this I filled with pea gravel as a draining floor, if left alone poo, and bedding would clog the gravel and it would not drain, so I use a garden tarp style black mulch fabric as a poo strainer, then straw bedding over that.
This way urine can flow down 12" below the foot surface, and the bedding stays very dry, if you treat the floor with compost tea the biota will breakdown the urine too and the urine and biota will balance out an ecosystem in the flooring material. Because of this you will not have the ammonia build up from the urea and you don't have to treat with lime to solve it. Occasionally I flood the floor to flush out the buildup ( after winter when biota are docile) and the water flows out below the barn in streams and seeps.
This is three years in and this spring cleaning had no smell, and the bedding on bottom is from November 22nd! Go biota! I wanted to wait to see the theory I had in action before I suggested it, but for me the jury is in after cleanup! And no matter how much rain I get it all flows below the barn passively without ever wetting the barn floor.
I designed and built my barn last year after a lot of thought and it is specifically designed for sheep and nothing else. It is an alley barn design, open on both ends by gates with a center divider and half wall down the middle. With numerous gates it acts as a sorting pen as well. It does have a concrete floor, pitching 2 inches in 24 feet to one side, with the sheep self-bedding daily. I clean out twice a week, but it is a breeze. We move the sheep from one side of the half-wall to the other, open the end gates, and the ones in the center then push through with the tractor. By being able to get the cutting edge between the manure and concrete, it scrapes up easily. This we deposit to the compost pile at the end of the barn. On the sides we built fold up hay racks that really have worked well. Being able to move, the sheep do not bust them when then rub on them but rather just push them shut. In this way when we clean out they are pushed all the way against the wall and allow full width of the barn.
It would not work well for any other animal, but we raise only sheep so it is specifically built. Our primary goal was health; getting the feed off the floor and being able to keep the animals off fouled bedding.
Diego Footer on Permaculture Based Homesteads - from the Eat Your Dirt Summit