The Zend Developer Zone has a new post promoting an extension for the Zend Studio/Eclipse IDEs called nWire that allows you to get a better overall view of the structure of your PHP applications.

nWire was designed for developers who get lost in large and complex applications. It dramatically shortens the time it takes to read and understand the code and reduces the learning curve for new developers. [...] nWire was developed with support from Zend Technologies and works with the new Zend Studio 7.0 and Eclipse 3.5 (Galileo) with PHP Development Tools (PDT).

The tool includes a visualizer to graphically browse the parts of your application, a navigator to see associations in the code and a quick search that makes it simpler to search the entire project. You can find out more about the project including downloads and a 4 minute intro video on the nWire website.