I put plastic on all sides of my run, and the top is about 80% covered, so it gets enough ventilation but still stays sheltered enough. I don't have a smell problem because I use a cold compost system, as some mentioned above - wood chips, dry leaves, and other yard waste, whatever is available seasonally I add periodically to the run. I bag and collect dry leaves and use them throughout the year. This neutralizes the nitrogen in the poop and it composts over time. The chickens stir it around when they scratch. It doesn't smell, get muddy, form puddles, or freeze solid in the winter. I wouldn't use inorganic material like sand/gravel/rocks in the run because it does nothing to compost the poop, the poop just sits on top of it or gets mixed in and it remains poopy and smelly. And cleaning it out is too much work and ineffective. My current setup is 4 years old and I haven't cleaned the run in that time - I haven't needed to, it looks like a rich and earthy forest floor.