We have the same problem with roots and rocks in our area, so we laid 18" of doubled wire on the ground along the outside of the run, overlapped the corners, and zip tied it to the chain link that was also lined with wire. Then used tent pegs and large rocks against the base of the run every few feet to help hold it all down. We did our fence the same way. It would take a strong animal to move those heavy rocks and so far so good. It was time consuming but gives some peace of mind knowing that if a predator wants to get in, we've made it MUCH more difficult to do so. Good luck!