You still have one vault left to do. It is the one with the possessed dwarf. Once you complete that, the quest should complete. The only loot from the quest comes from the containers in the vaults. Also, if the possessed dwarf survives, he will show you where he has some loot buried. You may have found the loot already. Typically, I do the vaults quest before the tree and Advocate. However, the order in which it is done doesn't matter.