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Shit happens, as they say, and if you don't deal with it, it will breed flies and other pests. And there are several great ways to use it. Compost it, feed it to BSF or worms. You can even give an herbivore's poop to an animal like a pig - it's just like grass and they love it.
If you have manure on your property, sooner or later there will be flies. They are one of the most irritating insects (besides mosquitoes) if you let them have their way. There are however many ways to control, and even use, them.