A particularly cleaver programmer can use PPI to map the code layout and GraphViz to create a image linking the code together.

Note: In this instance, I am not the clever programmer. A co-worker of mine did this for a C++ application and was able to delete 75% of the code the had in production (about 300,000 lines).

However, this is something you do need to be careful about otherwise you will be cursing yourself whenever something bad happens.