Hey Cyberwolven and DV8ER, good to see you both again.
I think what's interesting is when you look at the analog comparison of how a computer works vs. what we see in the computer world, you could interpret everything as logically lining up to be 1:1 with us doing something on the computer and that being carried out in the digital side. However, when a user gets thrown into the mix, anything they do is effectively like a program having its own will, and that can affect how the other programs function.
Going further on this, with a show like Uprising, where there's no user input and the programs are starting revolutions and derezzing each other, you could equate that to how computers tend to become unstable if left on for too long.
In the context of the most recent movie, Ares is already kind of a unique situation in the context of what we've seen up to this point - he's not a standard program but rather neural network AI (as we can see visualized in the opening credits sequence). Instead of a user coming to Ares' world, it's Ares coming to our world that sort of kicks off that erratic behavior that doesn't necessarily line up with the commands he's given by Julian, and eventually leads to him becoming fully human near the end.
I think the permanence code is what was on Flynn's disc at the end of Legacy, which allowed Quorra to be materialized without a time limit, and could be applied to any program. Though visualizing it as a double helix makes me think it's related to the core of the ISOs' collective programming. We also see that Eve is able to be materialized by the same laser without a time limit and without the permanence code present, so maybe
I did also want to talk about the mid-credits scene briefly: the impression I got is that the Sark 2.0 program isn't really a standalone program, but rather it's maybe designed to be integrated into a digitized user? A bit terrifying to think about, but Julian does seem to nervously know exactly what to expect when he grabs that disc. You could even say that it's a direct inverse of the permanence code, instead of turning programs into users it turns users into programs.
Just some stray thoughts!