Lore
Throughout the four editions of Shadowrun, no rule-set has been changed more dramatically nor inspired more complete house-rules than the Matrix section. And this is unsurprising, because the Matrix touches upon something which is somewhat real, computers, while at the same time living entirely in the realm of deeply speculative fiction.
But more so than that, the Matrix has always had a tremendously difficult problem with abstraction of action. That is, it is entirely possible for the game to model every single pull of the trigger on a gun, every invocation of a spell, every turn of a car, but it is not possible to model every machine language command that flashes by a hacker. Every time you blink your eyes, a quadrillion processes crank through to completion in the Matrix. Equations are solved, numbers added and lost, and even listing all of them that had passed during a heart's beat would be longer than every book ever written. So actions in the Matrix have to be abstracted. And yet, no past or current edition has had a consistent degree of approximation, which leads to painful and exploitable wrinkles in the game system.
At the beginning, a computer system that an NPC used was modeled as a separate "room" for each arbitrary part of the computer (I/O, Storage Memory, Graphics Card, whatever), while the computer that the PC used was modeled as a series of attributes which modified the "Decker's" matrix icon (Where I/O was a location in NPC computers, it was an attribute in PC computers). In 4th edition, all processor power is abstracted and programs run arbitrarily somewhere in networks. Except that you can also choose to count specific hardware as unique networks running their own copies of programs, and then each of the networks gets to take individual actions in the Matrix based on how many completely arbitrary divisions you've decided to have in your arbitrary computer network.
What is presented here is not the only method to realize the Matrix. Indeed, there are literally an infinite number of ways you could imagine it. Like Astral space, the Matrix does not exist; but unlike Shadowrun's magic, the Matrix isn't even loosely based upon folklore. What is here is hopefully a manner of realizing the Matrix which is consistent, playable, and fun. After all, if the rules are playable and they agree with the presented fluff to the extent that unplanned events can be extrapolated from the rules, then we can get back to what's really important: playing the game.
But before we can get some answers, we are going to need to formulate our questions.