You really don't need to clean out the run at all, maybe every 2 years or so. You aren't leaving it long enough to compost down. Are you adding shavings to earth? Just leave the earth for them to scratch in, poop and it composts on its own. You can hose the poops into the earth or dig them in if you wish.
If your run is really dry, they will just dry out and it shouldn't smell. If wet, it will compost where it is.
I think your cleaning regime is out of whack. Stop generating so much stuff to get rid of by cleaning the run out. Use deep litter in the coop and clean every few months. Poop tray poop can be bagged up and left for a few months to rot down, or chucked on your existing compost pile. That's only a couple of handfuls a day.