This entire section about powers endeavors to explain what specific powers people have and why. What the limits are and how they work. Fundamentally, we believe powers within the Matrix have explanations which we will try to get at.
Understand that in the explanation of the mechanics we are in no way suggesting that the user is specifically or consciously invoking those mechanics. Powers are invoked by will or reflex, but either way we don't believe that the user imagines these specifics anymore than you contemplate the mechanics of moving your arm when you type.
We must also remind you that this is a theoretical approach attempting to constrain and explain what we see and know. Just as we don't know if gravity is caused by gravitons, quantum mechanics, or space curvature these theories are here to provide a framework NOT a series of absolute facts. We will, of course, adjust theories as more information arrives.
Another useful concept is that of a singularity. Recognize that there are phenomena which are simply beyond our capacity to explain at this moment (not that cosmologists should stop seeking the truth)... times at which the rules we've defined- for example electromagnetic, strong nuclear, weak nuclear, or gravitational forces- break down and don't apply. However, the existence of singularities in no way makes those rules and concepts useless or worthless. By and large, the entities of The Matrix universe behave according to rules more than not.
One final concept. Physicality matters. Read about Neo limits for more on that topic. But essentially, physical interactions are much more powerful. Pills are ingested and injections given. The application of force comes through a fist. And so on.
The powers exhibited in the Matrix more or less break down into three categories: Human, Machine, and Technology.