I agree, though there is a lot of subtlety in this problem. I tried, with very modest success, to write a tool that would overlay some graphics showing these kinds of information on top of a regular code listing.

The results were rather satisfying when the structure to be illustrated was relatively simple, as it often is in well-written code. However, trying to use those visuals to help analyse and understand less well-written code with complicated, tangled flows felt like looking at spaghetti code in a very literal sense.

Qualitatively it made it obvious when code could benefit from some cleaning up, but that isn’t very useful information unless it also provides useful insight into how to clean the code up, and I never really found a style/format for the visuals that conveyed enough information to provide actionable insights but didn’t become so busy in bad cases that it became was hard to follow.

I know some editors specialize in novels by having wiki like features of linking characters to storyline and research work. I'm not sure how much of those are used by real world authors though…

I’ve only had this discussion with one author recently, but FWIW, they swear by that kind of structured story planning software. I’m not sure how many of the concepts or presentation details in those applications would translate readily to tools for working with code, though.