In the conversation between Neo and the Architect, the Architect tells Neo that the "Prime Program" will be reinserted after Neo's code is disseminated.
Every time a Matrix inhabitant rejects some rule within the Matrix, it causes an error within the Matrix. This error (or the way of thinking that caused the error) is then encapsulated (or summed up) into the code of the One. We know summation doesn't happen on accident, so the summation process itself must be a program. I believe the Prime Program is this encapsulation (summation) process. It may be an invisible program, or it may even be the Oracle since the Oracle is wired to all Matrix inhabitants and would certainly be aware whenever a rejection occurs. I strongly believe the Oracle is indeed the Prime Program.
More generally, I think the Prime Program has always been the operating system of the Matrix. Before the Oracle introduced her choice model, the Prime Program would have been simpler - it wouldn't have had to worry about a system of rejection and the One. After the Oracle changed the Matrix, it expanded the function of the Prime Program. More support for this will be given on the next page, Matrix System: Revision History.
If the Oracle is the Prime Program, that would bring more meaning to the idea that Seraph protects "that which matters most". What in the Matrix matters more than its own operating system? Not only would the Oracle's death make it impossible for the One to cancel out rejection to avoid cataclysmic crash, the Oracle's death would crash the entire Matrix.
My theory also makes the Smith-Oracle takeover make more sense: not only could smith see far into the future, he was also literally running the entire Matrix. That is why Smith laughed like a lunatic. It is also why the Oracle was the only program in the Matrix that Smith took over which resulted in a whirlwind in the room. This surely resulted from the fact that there are so many links and connections from various system components to the Prime Program - the whirlwind represents a massive reconfiguration of the system's interface with the Prime Program.
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