I am involved in leading the project to redevelop http://www.richmondgov.com which is the city government site. And one of the biggest problem that we noted when looking at the current site is that why is this or that, piece of code in this or that location.
We noticed that no one that designed the site in the past was still working for the city. This cause a lot of problems in that the reasoning for the file structure was totally lost.
So we started from scratch.
Mind you we are designing this so that it will live past the employment of anyone person.
So we are looking to have a logical divisions for the code that would make it easy to understand.
so there is a folder called root and in root there is four folders called Content, Behavior Design and BIN.
The other thing is that there is no direct link between the site navigation and the file arch so why tie the two together.