Jacob uses his praise of God as a foundation for his prophetic admonition. This is not prophesy, but counsel. It comes through his prophetic authority, however, and therefore has place as part of what Jacob considers his prophesying. Jacob plays off of the reading of the wicked who are to be cast off, the branches that are to be burned, to use that destruction as a call for repentance. His message is that there is great hope available but that it is only for the repentance. It is only for those who follow the Lord. Clearly Jacob sees in his people conditions that are leading them away from the strict obedience to God's way, and so he uses this ultimate division between good and evil as the impetus to his exhortation that they be found on the side of the good.
That the allegory places this event in the last days, and that Jacob certainly understands that the events to which the allegory alludes are far into the future, he nevertheless personalizes and makes immediate the message of repentance. As a people of Israel, the eschatological future will be as the allegory depicts it, but for the individual, such decisions are perforce immediate. No man who has received the gospel can assume that judgement comes only at some faroff point, and happens to far distant peoples. Each of us will come to our own individual judgement regardless of how the timeline of our individual lives meshes with the great timelessness of eternity. It is to our own individual salvation that Jacob turns, reminding his people, and through the, us, that we are accountable ourselves, and this ultimate judgement between good and evil for the world in general will inevitably happen for our own lives.
Jacob 6:6
6 Yea, today, if ye will hear his voice, harden not your hearts; for why will ye die?
The choice is between life and death, to be gathered in or cast off. Jacob's poignant pleas asks "why will ye die?" This eternal death comes because they will not repent, but repentance is a personal option. It is something over which they have direct control. Jacob knows that if they will give place to the word of God that it can work in them to salvation, but that this giving place is a personal decision. He therefore exhorts them to not harden their hearts. They need not die eternally, because repentance is readily available.
Jacob does not tell us what it is that would require their repentance. This discourse appears to come at a very different time that the discourse of the early chapters of Jacob. At the end of chapter 3 he concludes that first discourse with a very determined ending: "Jacob 3:14 These plates are called the plates of Jacob, and they were made by the hand of Nephi. And I make an end of speaking these words."
The intervening chapter discusses the plates and the reason for writing upon them, and now we have this sermon. It is quite likely that the problems explicitly discussed in his first sermon (pride and particularly the multiple wives) are sins that remain with the people. Jacob would not be the first, and certainly not the last, prophet to admonish his people and have only a limited effect upon changing their behaviors. In the absence of other specific sins, we may assume that the same conditions exist, and that Jacob continues to call to repentance, though no longer needed to elucidate the specific sins. They would have known what concerned Jacob, and the repetition was superfluous for them. It was the continued call to repentance that was important. If this hypothesis is correct, then the question Jacob asks "why will ye die" refers very specifically to their choice to continue practice which Jacob has declared against the will of God.