Question about scene in The Matrix Reloaded

I am a huge fan of the Matrix series, but for the life of me I just
can't figure out certain aspects of the scene between Neo and the
Architect. I'm posting this question here since I believe the answer
has to do with computer programming issues. Here is a copy of the
transcript from the scene in question:

http://www.ianua.org/comments.php?id=95_0_1_0_C

The main part that confuses me is when the Architect says that Neo must
temporarily disseminate the code he carries, reinserting the prime
program. From what I've been able to gather in the little bit of
research I've done, phrases like "prime program" and "anomaly" are
programming terms. However, beyond that I don't know what the
Architect is talking about. Is he talking about rebooting the Matrix?
What is the code Neo carries? Is it the prime program? A glitch
caused by people refusing the Matrix? Or is it something else
entirely? Help!

I'm hoping someone in this group who is a programmer and is also a fan
of the movies can help me understand this scene (and any other aspects
related to this scene). I'm not a programmer, though (hence the reason
I'm here), so please explain it simply and in laymen's terms if at all
possible. Any help that can be provided will be greatly appreciated.

Thank you