I use several inches of shavings in my coop, which has a woodenfloor. In my run I have a base of what is called around here "Class I" sand which looks like a mix of finely crushed stone and sand. Over the Class I in the pen is several inches of shavings. I have Cochins, Brahmas and Faverolles and even their feathered feet stay nice and clean. I have developed a system now where, when I need to clean the coop out (about every 3 months) I simply pitch the shavings out the door into the pen and spread them around. Then add fresh shavings to the coop. Originally I planned to move the shavings from the pen to the compost heap or garden whenever they got too deep; however, I have found that the shavings are breaking down much quicker than I expected and I assume are getting scratched into the sand layer. At any rate, I have yet to have to remove any of the shavings from the pen and I have had no problems with mud or the shavings getting stinky and I've been doing this for the last 8 months.