Source Code Directory Structure

As the topic description says, both VC2005 and VC2008 have a limit of 90 /I# options. the CMakelists.txt for the worldserver currently has 94 includes. now every one loves descriptive directories for all each part of the source, cause it makes it easy to find what your working on. my question now is what would it take to redo the entire directory structure for the source so that issues that vc2005 and 2008 have can be avoided or fixed? besides someone actually moving files that is?