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You don't need to do this from the var directory. I work with the classes directory directly. And yes using IDE otherwise it will be impossible to follow the code.
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Indeed Steve, I noticed that as well in 5.4.0.6. I can trace code from inside the /classes directory. According though to the developer's articles, the php scripts are executed from inside the var/run/classes directory after they have been cached by the decorator during a store re-deployment. So, I wonder how come the tracing in the IDE can take place from inside the /classes directory, which is of course is a good thing.