The action of these verses once again suggests the care and patience of the Lord. An action is take to preserve the tree (or more properly, the "roots thereof") and then the Lord allows time to watch the effect of the action. After the initial major action, there is more digging and pruning and nourishing. Thus the Lord may take major actions, but will also then return to a time when our agency becomes the foremost dictator of action, and the Lord awaits to see the fruit that we will produce on the foundation he has provided.
Note the allegorical distinction between tree and roots. Once again the trunk is a collective designator, but the critical element is the root. The Lord of the vineyard is not taking care to preserve the tree, but the root. For the Lord, it is his covenantal relationship that is the important aspect of his relationship to man, not the particular race of men who become 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.
Jacob 5:13
13 And these will I place in the nethermost part of my vineyard, whithersoever I will, it mattereth not unto thee; and I do it that I may preserve unto myself the natural branches of the tree; and also, that I may lay up fruit thereof against the season, unto myself; for it grieveth me that I should lose this tree and the fruit thereof.
The antecedent for this verse is the young and tender branches mentioned in verse 8. The allegorical action is to take the branches of the tree and use them to plant trees in other locations.
Botanical: One of the interesting aspects of the allegory from an naturalistic viewpoint is the planting of branches. Hess et. al. note:
"The olive is one of the few fruit trees that can be propagated by taking a branch of a tree and burying it in the ground. This is apparently what Zenos had in mind when he indicates that the Lord of the vineyard took branches and "planted" them, saying that the natural branches were "hid" in the ground (Jacob 5:14). Hillhouse states that the olive is extremely tenacious. When the trunk has perished by frost or by fire it forms new sprouts. If a bit of the bark, with a thin layer of wood, is buried in the earth, it becomes a perfect plant. All of the branches and even the trunk can be removed and the tree may still live (see question 19). Olive shoots can be cut off, placed in soil, and indeed they will root." (Hess, Wilford M., Daniel J. Fairbanks, John W. Welch, and Jonathan K. Driggs "Botanical Aspects of Olive Culture Relevant to Jacob 5" In: The Allegory of the Olive Tree. FARMS, Provo. p. 530).
Symbolic: The nature of the young and tender branches was that they grew in response to the less drastic original measures of the master of the vineyard. As was noted, they represent those who heard and headed the words of the prophets. The history of Israel has many examples of divisions in the religious understandings of the collective people, a process that is much better understood with the discovery of the Dead Sea Scrolls and the subsequent scholarship that has attempted to clarify the nature of the historical people who preserved them. As was noted above, both that community and the Lehites are examples of peoples called out of Israel. The Book of Mormon also preserves the story of the Jaredites, who also fit the "called out of Israel" model.
In this part of the allegory, some of these groups are called out of Israel and sent into the world. The master tells the servant that they are sent: "whithersoever I will, it mattereth not unto thee." We understand from this that while we may know of some of these peoples, there may yet be others of whom we are not aware. Our current historical ability to list the Lehites, Jaredites, and the people of the Scrolls as types of these scattered branches suggests that they may have occurred at multiple times and in multiple locations. We will see as the allegory develops that we are certainly missing the historical reference from some of the "young and tender" branches.
Polemic: The idea of planting branches works for the allegory of the olive tree, but does not work for many other botanical species. It seems rather unusual that a modern creation would include this rather odd element which fits only into the culture of the olive, with which Joseph should not have been familiar.