what are the clues in chapter 7,8,9,10,11,12

I can't go through each clue but I can mention a couple:

Holmes realizes they are indeed dealing with a real dog, not a phantom because the new boot was returned after it was stolen from the hotel and then an old boot was stolen.

The convict, who was wearing some of Sir Charles' old clothes was attacked by the dog. Could this have anything to do with Sir Charles's scent being introduced to the dog.