[samsquire]

We need tools that process command line output and large files and create tables of contents dynamically based on rules of architecture or comments and allow efficient navigation. I need overlapping buckets or tags.

I've been thinking about it lately but what I've seen in IDEs is not what I want

I liked OpenGrok

[WillAdams]

Are you willing to do that by hand? Have you heard of the author of _The Art of Computer Programming_ and the technique he created: Literate Programming?