we are going to be putting in more grass clippings and leaves just need to wait for the rain to stop so we can mow. LOL I think most of it came from where the plywood meets so has a gap so once that is shingled it won't be an issue any more. The part of the run with out a cover didn't have any mud that I noticed it was in the roof covered part since the plywood didn't meet up perfect.Sorry about the dog. If you can get more litter materials, that'll help with controlling the mud. It's fine if feathered feet get wet or a little muddy, but you don't want them becoming mud balls, so anything that'll keep them out of the dirt (which is then mud if it rains) will help.
They weren't mud balls just really dirty feet.