How do I prevent rain entering around branches/the trunk that pass through the treehouse?
Try to avoid this if possible. It is hard to get a good seal around a branch or the trunk if they pass through the wall or roof. The seal needs to be flexible to allow plenty of movement of the branch (a gap of 2″ is a good start) so most successful methods involve using a neoprene collar, using black mastic/sealant for extra gap filling properties.