I haven't done this on very large code bases, but I've had good experience using Simon Willison's showboat to make the model deeply inspect the code, using variations of the following prompt:
> Read the source and then plan a linear walkthrough of the code that explains how it all works in detail. Then run “uvx showboat –help” to learn showboat - use showboat to create a walkthrough.md file in the repo and build the walkthrough in there, using showboat note for commentary and showboat exec plus sed or grep or cat or whatever you need to include snippets of code you are talking about
Asking for plant UML diagrams, and invoking the the spirit of Knuth and McConnel are also useful
> Read the source and then plan a linear walkthrough of the code that explains how it all works in detail. Then run “uvx showboat –help” to learn showboat - use showboat to create a walkthrough.md file in the repo and build the walkthrough in there, using showboat note for commentary and showboat exec plus sed or grep or cat or whatever you need to include snippets of code you are talking about
Asking for plant UML diagrams, and invoking the the spirit of Knuth and McConnel are also useful