In both eclipse and netbeans, a prerequisite for debugging is that the project is built.
"Building" doesn't do anything real: php code is not compiled. But it allows the IDE to build a dependency tree, validate the code, allow code completion and follow execution flow from one class to the next.
To build, in eclipse either right click on the project or choose Project/Build from the menu. I have set Build automatically so the resources stay in sync while I work: