I have a similar issue.
We are cleaning up and redoing humungous site (at least 500,000 pages) that still has code dating back to the last century. There is inline css, css directories and include directories everywhere in the sprawling structure.
So we plan to break it up into separate sites, but with common things like footers, a global nav and similar page structure and framework files. We are using Foundation 4 with SASS (don’t get me started on F5).
In reaction to the nastiness of the existing site, there are those that want to structure the code like this:
/includes/site1/(site 1 includes)
/includes/site2/(site 2 includes)
/images/site1/(site 1 images)
/images/site2/(site 2 images)
I think this is madness – and it will drive me crazier than that awful gif in @NIX’s last post. :^)
I would rather see global/framework stuff at the root, and includes/css that is specific to the subsites at the root of that sub site, and images relative to where they are used.
The other question – where do nav includes go? A /nav/ directory or under /includes/