The concept behind Zend_Debug_Include is that the dependencies for each source file are stored in a separate file. If the source file is modified, the file containing that source file's dependencies is rebuilt. This concept enables you to determine run-time dependencies of files using arbitrary components. This solution is also useful if you are deploying your application using Linux packages.

He has it broken up into a few different kinds of tracking examples - file dependencies, package dependencies and external dependencies. There's also a tip for the URL adapter showing how to make a different file for each request that comes through.