As someone who has seen several LARGE commercial software projects, there is a definite gradation from "it's hard to comprehend these layers of abstraction, but after a few days I kind of understand how they interact" to

    // X - uncommented on 1.2.03 to fix bug
    // Y - commented again on 3.2.03 because it broke stuff
    // if (condition)
    {
       ... logic here, half of it commented out ...
    }