when you finish talking to the tree and it gives you a seed to plant on the top of the mountain for in exchange for wood
I guess that you're missing an idea how to get the seed up the mountain, since you can't get through the door on the mountain base? The trick is to throw the seed up the mountain at some of the vantage points. There are signs that hint at that and the throwing-item-npc will talk to you about that as well.
If you have any other problems, you can always just check a let's play to see how other people managed to overcome the obstacles. e.g: