Do they have an outdoor run? Can you move their water out into the run? Only do this if you are able to let them out for fresh water just as soon as they come off their perches in the morning. Can you move their feed out into the run? What style feeder are you using, and what type of feed are you giving them? I do a deep litter in the lower level of their coop which consists of hay, leaves, and grass clippings. During the winter, i kept their feed and water in the lower level, setting it up on a pallet to keep them from kicking so much litter into the feed and water. Unless we've been in a deep freeze where mid day temps in their sun room did not get above 20 degrees, i gave them fermented feed. If the weather was colder than that, I gave them crumble. But, i can tell you that they prefer FF, and their poops do not smell and are not as nasty when they are on the FF. Just as soon as the weather warmed up a bit, i moved their feed and water out into their run. They get FF 2 - 3 x/day, and they lick their bowl clean. Their poops melt into the DL in the coop. So, the flies really don't have much of a breeding ground. Check out the fermented feed thread. It's super easy to do, and gives your flock an extra nutritional boost. I suspect that your girls are billing a lot of feed into the shavings, and mixed with the water they are spilling, it makes an excellent breeding ground for flies, not to mention an attractant for rodents. Fermented feed will save you a whole lot of money b/c they will not waste so much as a grain of feed, and the feed that they do eat will go much further.