My neighbour has gained planning permission (ownership is not considered). I believe that he cannot legally proceed, but how do I stop him?
You both must have a contract that you signed. There must be a clause in it that says you both have to agree to something before you can proceed. If he wants windows on the roof, let him. Tell him you aren't paying. He cannot force you to pay for them since they are only cosmetic and not something that has to be done, like a new roof.
