don't the chickens dig threw the gravel, down to the ground?
It depends on how thick the gravel is but in general yes, they love to scratch. What do you consider to be the problem with them reaching the ground? It’s normal and natural for them to scratch in the dirt and peck at it. They get grit that way and find various things to eat.
how would you pick up the poo?
You don’t. Not everybody tries to pick up the poop or even needs to. We are all unique in how we manage our chickens and how we need to. We have different set-ups and climates. Some people never clean their runs, some really need to regularly. A couple of important factors in that is the chicken density. The smaller space you have them in the more the poop builds up. They are going to poop wherever they are so the more they can spread that out the less likely it is to build up to a problem level.
The other very important issue is drainage. If the water drains away from the area so it stays dry or quickly dries out after a rain or melting snow you generally don’t have big problems. Dry poop isn’t that bad, wet poop can be horrible. If your area is fairly small the poop may build up so it never dries out, even with good drainage. With good drainage some people might use a hose and wash their gravel so the poop is washed away. If you don’t have good drainage that could cause it to stink. If water stands there instead of drains away you are probably going to have problems no matter what bedding you use in the run.
My guess is that you have a small suburban coop/run. Gravel would not be my choice for bedding in the run. You can’t really clean it and if you have to remove it that requires a lot of hard work. Plus where do you put it if you remove it? It works for some but I’d use something else.
My main run is just bare dirt. It’s on top of a rise so it drains well plus they have a big area outside the run inside electric netting so they aren’t in the main run that much to start with, not a lot of poop gets dropped in there. I never clean my run. I’m not suburban and have lots of room. In suburbia some people use sand, PDZ, or something else in small runs to make it easier to scoop the poop. Some are able to turn their runs into a compost pile. They toss organic material like wood shavings, dried leaves, straw, hay, grass trimmings, kitchen and garden waste, anything that will compost and let the chickens keep it turned for them. There are all kinds of different ways we go about solving these problems.
I don’t know what your run looks like, some photos could help us come up with a practical way to solve the problem of them digging down at the edges to allow mice or possibly other things to get in. One way to stop them from scratching right at the edge to create holes a mouse could get in might be to use an apron made of small mesh hardware cloth on the outside of the run. Not sure how well that will work with mice since mice will tunnel, not just dig under a fence like predators. The mice will be attracted to the chicken feed so a more effective mouse solution may involve not leaving the feed out at night. Mice are a pretty common problem and they can be hard to manage.
