I have a large web app, and I think there are a bunch of old files that are no longer being used, is there an app which can tell me what these files are?
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There is also the Dead Code Detector (DCD). It finds functions that are never called, which may help to clean up even the files you keep in production.
You should be able to start with your web server logs. These will show you which files ARE being used. From there you should be able to track down a good number of the files those reference. Don't know of a good way to find out which aren't being used, only those that are.
I think you need to check out the project management tools available for php.
You can have a look at phpUnderControl (http://www.phpundercontrol.org/about.html) and CruiseControl (you can google it).
You can also use a tool (i.e and IDE) that will give a Code Coverage Report.