I just checked out a PHP project (SAHANA), opened it in eclipse PDT, and found out that the code navigation is not working. I couldnt view a function’s code by just ctrl+click ing on the function call.
Asked Ravindra and this is the solution he gave me.
What I did was just created a new dummy PHP project named test in eclipse,
got the .project file which was generated in the project folder (test) and copied it over the .project file I had in the project (sahana).
Opened up the newly copied .project (in sahana) and edited the <name></name> to match the name of the project (say sahana-phase 2).
Closed and re-opened eclipse.
BINGO!!! now I have code navigation.
Ravith's Blog 
Ravi’s method is working, Alternatively what you can do is use Eclipse PDT (PHP Development Tools),
http://www.eclipse.org/pdt/
It gives code navigation out of the box plus other cool php base features.
You do not want to close an reopen. just refresh the project by right clicking on the project name. 🙂