Having previously argued that programming is literally writing, I think there's something to this idea (even if I do find minimaps helpful sometimes).
What would a table of contents look like for program code? While we're at it, how about an index?
Glossaries also present some attractive possibilities. Think of every codebase you've ever encountered where you were like “OK but what does a _____ actually do? What does it mean to ______ a ______?”.
Figures and tables are already in use in some limited ways. How can we expand this? (Figures presumably would mean images embedded in comments. Does anything support that yet?)
If programming is writing for humans first and the computer second, which it is, then what tools do we use, what facilities do we provide, in writing for humans-only that we ought to bring in to programming?