If you use a test coverage tool, it will tell which ones are definitely used,
for whatever functionality of the software you have exercised. (Obviously, the more you exercise
the software, the more of it gets executed by the non-dead part.). This includes any file accessible via an external html link; of course, you have to exercise that link, as it is part of your application functionality.
Then you can inspect the ones it says are not used do decide what the case really is.
Our SD PHP Test Coverage tool will accept a list of all the files you wish to check out, and enable you to easily collect such test coverage data. It provides a summary report showing which files have any coverage at all; those with 0% coverage are the ones that are likely dead.
