See the SD PHP Test Coverage Tool. You exercise your code any way you like, including (or not) running test suites any way you like. At the end of execution, you can see a display of what code was executed (there are screenshots at the website). Code that is not executed may be dead, and requires some more analysis on your part, but if you exercise the system well, unexecuted code is either error handlers or really dead stuff. The PHP Test Coverage tool does not require any changes to your PHP server.
The SD CloneDR tool finds duplicate code across very large source code bases. It is language sensitive (covering C, C++, Java, C#, Ada, Fortran as well as PHP4 and PHP5) so it isn't fooled by changes in formatting, whitespace or the presence or absence of comments. It will detect exact copy clones, and near miss clones. The website shows example clone reports for several languages.