I just fixed the smell in our coop and run. Up until this year we never had an issue, however the number of birds (13) and the endless spring and summer rain and the shade from vines on the run all combined to produce a constant and pervasive odor. The neighbor closet had guests today and asked if something could be done.
We had shoveled some of the top layers, soil with a lot of oyster shells, and built up chicken waste and food. That still didn't do much as the ground is wet from rain and the anerobic bacteria really has taken hold.
I thought about what to do, limited time (due at a 4th of July party). I laid down two gallons of simple green a non-toxic deodorizer. I did not want to use bleech both for concerns over the birds and not wanting to kill off biology digesting the waste. Next we dumped in a layer of charcoal (no added chemicals you could make it, but given the time we bought it on sale at wal-mart). The charcoal abosorbs odors, helps aerate the soil and does not add to the rotting material. We then added a layer of baking soda to further deodorize and to help neutralize the soil. Over everything we added a layer of pea gravel to keep everyone out of the mud. This took about an hour in including trip to Walmart and with one kid sort if helping. Cost $50 for a run about 25 x 8.
Next we will add sand and more gravel. Problem solved. I am also making a chicken tractor to get them out for grass and bugs and reduce the build up in the run. We also cut back the overhead cover to get more sun in.