I agree with your initial point: A single explicit hierarchical structure will never please everyone all of the time: There are too many implicit relations that

I agree with your initial point: A single explicit hierarchical structure will never please everyone all of the time: There are too many implicit relations that could (and arguably should) be captured. It might be tempting to try to maintain multiple directory structures, making use of hard or soft links into the code base, but this sounds like it might be fragile, not to mention hard work to maintain. I am sure others have also tried to abandon hierarchical file systems altogether, placing the design into a database instead. This also seems like a lot of work, although I can see the attraction. My solution is to embrace the conflict and take an opinionated approach to the hierarchy -- one that enhances and supports the development process -- but to supplement that with generated HTML documentation with multiple different hyperlink-based navigation schemes. At some point, I also plan to integrate a javascript text editor into these HTML reports, at which point the whole contraption will have transmogrified into a sort of Kentucky IDE.