I use the deep litter method and normally clean it once a year. My coop is more of a house ( 16'x24' )and roost poles can hold 135 but at the moment I only have 20. I just scoop out the litter and put it in the garden. I don't disinfect the floor because that would kill the bacteria that breaks down the litter. Never had any problems with flies or smell. They only sleep in there, during the day they free range.
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