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In <http://ant.netbeans.org/source/browse/ant/freeform/src/org/netbeans/modules/ant/freeform/FreeformProject.java.diff?r1=1.32&r2=1.33> the filtering of merged lookup was commented out. Once the issue 53058 is resolved uncomment it again.
Fixed in: src/org/netbeans/modules/ant/freeform/FreeformProject.java; new revision: 1.34; previous revision: 1.33 test/unit/src/org/netbeans/modules/ant/freeform/spi/ProjectNatureTest.java; new revision: 1.4; previous revision: 1.3
Verified.