I'm stuck on the root removal quest. Where do you use the root poison? I did fight two of the root bundles before getting the poison, so that might have messed things up.
If you have the poison, it should have given you the option to poison the root. then you would have had to fight it.
If you don't, the root will never die.
There is also more than one root. Next to the house, there's one giant root. Granted, that was before the world got updated, so maybe I'm wrong.
But before initiating the fight. It should ask if you want to poison the root.