There's a great tool called doxygen which you can use to generate documentation from source code, including lists of functions in files, call references, file inclusion references and the like. You can see the documentation generated for Marlin at www.3dkarma.com/Marlin/html. Click on the Files link in the navigation tab, then keep expanding the tree until you get to the list of files.

The quality of doxygen's output is dependent on how will the code is documented in-line. Unfortunately Marlin doesn't have much in the way of in-line documentation, so you won't see much descriptive information in doxygen, but you will at least be able to get information on what's where and what gets called where and by what.