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If you rename project which contains other projects in the project folder, these projects are deleted. To simply reproduce it just create Enterprise Application project, let Create EJB Module and Create Web Application Module check boxes checked and try to rename the Enterprise Application project. EJB and Web Modules will be deleted.
Caused by rewrite from Files to FileObjects, I am already fixing it.
Fixed: Checking in src/org/netbeans/modules/project/uiapi/DefaultProjectOperationsImplementation.java; /cvs/projects/projectuiapi/src/org/netbeans/modules/project/uiapi/DefaultProjectOperationsImplementation.java,v <-- DefaultProjectOperationsImplementation.java new revision: 1.2; previous revision: 1.1 done Checking in test/unit/src/org/netbeans/modules/project/uiapi/DefaultProjectOperationsImplementationTest.java; /cvs/projects/projectuiapi/test/unit/src/org/netbeans/modules/project/uiapi/DefaultProjectOperationsImplementationTest.java,v <-- DefaultProjectOperationsImplementationTest.java new revision: 1.2; previous revision: 1.1 done