You could find or write a script that lists a site's contents if your OS doesn't have a tree. I find my Windows * search does a list OK, but it isn't quite as easy to see relationships. Folder and file names usually give some clue as to what they hold or do.
Starting near the top level folder I would try opening the files in a text editor (not running by mistake!) to see if they were binary or text. The .htaccess file is ~#1 as are any "config" files I might see.
If they're text, then the hard part. It takes understanding of the language to see and pick apart enough to follow up on things. But I guess most languages have a way to "include" code from elsewhere.
Get out your scratchpad and open your clipboard, I'm willing to bet you'll need notes to keep track of options and "leads".