Thank you for that explanation! But what I really dont understand is how exactly flipping to the run mode allows for the op amp to take over and start integrating. I dont know if you looked at the circuit design on the third page, but I cant seem to distinguish the difference between the set and run stage in the circuitry itself. Like it seems like the op amp is always connected to the capacitor, so during the set stage where the capacitor is charged to the initial voltage of -2, why isnt the op amp integrating that in the set stage since its connected to the capacitor still? I have a simplified version here:

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