Smell, mostly. Also muddiness of it, if you're using deep litter for example, and it starts getting muddy/mushy, then you need to add more material or replace what's there if more cannot be added without removing some first.Oh wow ok very interesting. How do you know when it's time to clean the run instead of adding more material?
For the wire mesh in the run: we installed it to protect from predators BUT we're just realizing now that the chickens will get their nails caught and so we're going to course correct and do as you suggested.

That's a lot of gravel! I can see why it'd be problematic to remove it.We didn't remove the gravel because the previous owners of the house had this whole big patch of the yard FILLED with gravel. There's like a foot deep of gravel, maybe even more. I have nowhere to put this and it's just too labour intensive. I'm going to add lots of material on top and hope for the bestshould i add both dirt and wood chips, or just tons of wood chips? thank you for all of your advice!
I do wood chip based deep litter. If you have space to store a pile of chips that's a very efficient material to use. If possible, could you build up the base of the run taller (i.e. add another row of boards under the current bottom of the frame), to allow for more volume of litter? That would help with "holding" more poop as well as give the chickens more layers to dig at. Not sure what the clearance is under the coop right now, but deep litter can build up pretty easily, like a good 6-8". So if the clearance is 12" you're looking at a space under the coop of only 4-6" once the litter is in.