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Let's say that: You enabled the option 'Apply code changes after save' in the configuration of the Java debugger. You have an Ant Java Web project and a dependent Java SE Project. The Web project has Deploy on save enabled. Both projects have the Compile on save option enabled. In the Web project you have a Servlet called HelloServlet that invokes a class called HelloService located in the Java SE Project. Debug the Web project, Do some changes to the HelloService class, save the file and you can see 'Apply code changes after save' doesn't work