Cleanliness is a habit of staying neat and tidy, or sterile. Cleanliness in your bedroom is nice, but cleanliness in a hospital operating room is critical.
If your friend remarks on the cleanliness of your locker, it's probably because of your thoughtful, color-coordinated organizational system. And if that same friend questions the cleanliness of your socks, it's probably because your feet smell terrible. Cleric John Wesley, one of the founders of Methodism, is famous for the line, "Cleanliness is next to Godliness," implying that how clean or dirty you are is a reflection of your moral character.