Something is digging under the coop and into the run. We've been having a fox problem and had to fortify the run. I've been checking it everyday to make sure fox is staying out. Hole is too small for fox and isn't getting chickens. Had an egg eater we had to cull (caught her with egg in beak! ) Have had broken eggs since then and thought we had another egg eater, but am now wondering if whatever is getting in there it's eating them, or the feed. Attaching pics of hole. Sorry about the cigarette, but didn't have anything else to give scale of size of hole 
