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If you use the GUI to add a classpath element to a freeform project which acc. to AntArtifactQuery matches a known project build output, then the <subprojects> element should be created in <general-data> if necessary and a <project> entry added. This would make it work somewhat similarly to j2seproject's, without any special user action.
Workaround is to add such a section manually in project.xml.
Fixed in: src/org/netbeans/modules/ant/freeform/FreeformProjectGenerator.java; new revision: 1.28; previous revision: 1.27 src/org/netbeans/modules/ant/freeform/ui/ProjectModel.java; new revision: 1.6; previous revision: 1.5 test/unit/src/org/netbeans/modules/ant/freeform/FreeformProjectGeneratorTest.java; new revision: 1.14; previous revision: 1.13
This issue was solved long time ago. Because nobody has reopened it neither added comments, we are verifying/closing it now. If you are still able to reproduce the problem, please reopen. Thanks in advance.