The Infestation

That cute little adorable rat is now dead- I killed him. I had an introspective moment after doing so; it's the first time I intentionally killed something larger than a bug. I suppose I'm experiencing some ambivalence regarding it.
When I built the coop and run, I did not plan for rats; I planned for raccoons, cats, hawks, eagles, and dogs. When I first discovered the rat, I had no idea how to handle the situation, how to prepare, or the severity of the problem. I figured correctly that the rat had come in from under the coop; the only area that did not have a subterranean border. I dug this area out and and laid down chicken wire. I came out later that day to capture the above picture. I was very self-satisfied thinking I had foiled the rat and solved the problem. Later that day, I went out to check and saw that the rat had found his way inside. I sneaked up on him ninja-style and took his life. I still don't know for certain how he got in; I thought it may have been through the overlap in the chicken wire that makes up the run. I wired that overlap tight and again I was confident the rat problem would be only a memory. I was very wrong and realized that there was a colony of rats living under the coop. They dug a network of holes under the chicken wire and were stealing the chickens food. Not only were they digging under the chicken wire, but the small ones could fit through the chicken wire mesh.
I got the great idea of inventing a rat trap. Here is a picture of it. So far, it has caught nothing, though, it appears no rat has even attempted to go near it as the bait has remained untouched. I dug all along the run, about 18" deep and put in a barrier of 1/2" hardware cloth. For a couple of days this seemed to work, but then I saw that they had managed to dig under that as well.
There was more that I tried to do and I won't go into everything but I was getting disillusioned with this whole thing and even briefly considered getting rid of the chickens. Eventually I dug out the entire run and laid down hardware cloth, attaching it to the run walls. So far it seems to have worked, though I'm not convinced; we still leave no food in the coop overnight.
Another problem we were having has to do with rain. The run became nothing more than a big mud pit. It was a precarious adventure just walking in there it was so slick. To relieve this, I attached a tarp to the garage wall (which the run and coop border)above the run and stretched it across the chicken wire roof and affixed it to the side of the run. This has worked great but blocks out the sun on nice days. I solved this by running 3/8" x 10' rebar through the eyelets at the bottom of the tarp. I can now use the end of the rebar I can reach to lift and fold back the tarp.