I recently took over a very old and large website that has about 800+ php modules. I wonder if a lot of them are even being used.
Is there a php cross reference tool to tell me which modules / functions are not used? My only option at the moment is running a Search --> Find in Files via Notepad++ and it is taking too long. 
This looks like a good place to start
I would also suggest using a proper editor / IDE, like Netbeans.
I am using NetBeans but I didn’t see an easy way to search through the project until now. Ctrl+Shift+F ;D
I found an entire suite of tools at http://phpqatools.org/. I am looking at Mess Detector and Code Sniffer. The tools appear to be installed in NetBeans which I tried to configure them. Unfortunately, they’re not working at the moment.