The action of these verses once again suggests the Lord’s care and patience. He orders action to preserve the tree’s “roots,” then allows time to determine the effect of the action. The initial major action of grafting is followed by more digging, pruning, and nourishing. I read this as a description of the Lord’s intervention, invariably followed by a return to a time when our agency determines our response to that action. The Lord waits to see the “fruit” that we will produce from the “root” that he has provided.
The allegory differentiates between tree and root. The trunk is a collective designator, but the critical element is the root. The Lord of the vineyard is taking care, not to preserve the entire tree, but the root. The important aspect of Yahweh’s relationship to humankind is his covenant with them, not some particular group who becomes attached to the collective designation as “tree,” or “Israel.” Whether literal or adoptive, Israel is the covenant people, and it is that covenant relationship that is being preserved.