For what it's worth, generally speaking I read all of the code and keep it in my brain - I have some uncommon assets in that regard like a high reading speed and great memory. `git grep` is the other tool I use often.

I rarely find that the call stack is the limiting factor, to me, and I suppose I do something similar to what you're talking about but just in my head - I know where a file is referenced via imports, what a function does, and what the flow of control is like.