As far as flies go, so far so good.
In early spring I was a little concerned because they were all over the outside of the coop and run, but I think, only to catch the warmth from the sun.
I use deep litter in the coop and clean the poop boards daily. The pop door is always open, so there is hardly ever poop on the floor. So far it is clean, dry, and odour free in there.
The run is covered, so it stays dry, and is also scooped daily. The chickens are in there for a couple of hours in the morning, then in and out at will until dusk, so after cleaning in the morning it stays pretty good for the rest of the day.
I throw a bag of fresh grass clippings in every week after taking the previous weeks worth out to the compost pile, which helps absorb any poops I might miss. I rake the clippings into a pile every morning, and the girls spread it all over the run by the next day. Because it stays dry, it breaks down quickly from the scratching it becomes quite a bit finer and mixes well with anything moist and helps dry it out. Whenever I'm in there, most of the girls have to come and see what's going on, so one of them is usually throwing the clippings around by the time I finish cleaning them up.
I didn't plan anything this way, so far it's all luck.
