We have a chicken tractor styled coop/run. The floor of the run is dirt, pine shavings in the coop. About once a week I am mixing around the pine shavings and adding a little bit of fresh on top. I also throw in some scratch to let the chicks do some of the work as well. However the last couple days the run has started to smell like ammonia. What should I be doing to keep the run clean, rake? put sand down? I think I am confused at how deep litter method works.