The story now begins with the essence of the plot. The Lord sees the decay of Israel. The response is not anger, nor an impulse to destroy, but rather a care to salvage. The pruning, digging, and nourishing are attempts one would make to cut back the decayed wood so that the remaining life tree's life force is concentrated in the support of the "good" tree rather than the old decayed part.
Assigning a more comprehensible value to this image requires us to find something in the relationship of God to man that provides this nourishing, digging, and pruning. It would seem that this is descriptive of the efforts of the Lord to send prophets with messages of comfort or calls to repentance, to either nourish our prune us, as we require.
The repentance process, if followed, prunes off the "decayed" part of Israel because it turns to the Lord, and is no longer "decayed." The word of God to the prophets also nourishes those who are obeying God. In this action of sending prophets to Israel, the Lord accomplished that which a gardener would in the process of pruning and fertilizing.
It is also important to understand that this is the logical first step in re-establishing a tree. It is a step that can have effect, and is less invasive or drastic than those efforts that will follow. Along with the specifics of the historical reading of this allegory, the spiritual reading is the care in which the Lord will nurture all of his children, and that he will call us gently to repentance before giving his children more drastic witnesses of their need to repent.
Literary: A final note is the mild emphasis in verses 4 an 5 on the promise/fulfillment set. In verse 4 we have the "word" of the Lord, the declaration of intent. In verse 5 we have the accomplishment of that intent. The explicit paralleling of intent/fulfillment highlights the trustworthiness of the Lord. What the Lord says through his prophets will come to pass, just as this master of the vineyard promises, and then fulfils that promise.