It's still valuable to deeply understand parts of a program, but we don't have any tooling that helps us do that. We just have to raw-dog it by thinking really really hard and remembering how all the code connects together.
I want a tool that gives programmers a place to record their thoughts. Developers need a place to draw and write, and also interleave blocks of code that automatically update to match the actual state of the code.
The closest thing I know to this is org-babel, part of Emacs, which allows you to push code blocks out of an org file into an actual source files, or pull them in from actual source files. This is mostly done manually by invoking functions called `tangle` and `detangle`.
I intend to investigate this further in Emacs, since I'm an Emacs user, but Emacs is never going to be the friendly UI we need to make this tooling common.