After I had cleaned it out well, I would get a bucket, add about a third of a bucket of lime then fill up to 2/3 bucket with water, mix it well, add about 25mls of jeyes then leave it to stand for about a hour after which I would stir it well. Then paint it on all the inside surfaces of my shed. Walls, ceiling, nest boxes, etc . Not only will it kill most of the nasties it wil brighten it up no end.
Added as an after thought leave it a day for the white/Lime wash to dry before adding your hens..