I'm using GWT as a front-end and PHP as a back-end in my application. I have those as two separate projects in Eclipse. My idea was to debug the application as a whole and I succeeded that. The problem is that I have to rewrite my ajax calls with Zend Debuger's parameters (DEBUG_SESSION_ID, START_DEBUG, DEBUG_PORT ...) every time I start a new PHP Debug session. That is because Eclipse produces DEBUG_SESSION_ID increased by one every time I start new debug session for PHP project.
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thats probably hard-coded into the Zend_Debugger. I don't think you could change that.

Thom Wiggers
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Yes, probably. I started to use XDebug few days ago and I think it is better then Zend Debuger when used with Eclipse. – Curi Jan 20 '10 at 21:06