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[ BUILD # : 200711261600 ] [ JDK VERSION : 1.6.0_03 ] Our project has sources and classes in the same location (just like it is default with NB 3.x and also when using javac from the command line). This scenario is no problem in Eclipse! Since NB 4.x, we always have to do a lot of customizing and still it is not "officially" supported. We always have to do 2 changes: 1. Ignore .class files in file browser, see issue #123723. 2. Change build.xml like this: <target name="-post-clean" depends="init"> <echo message="Deleting all classes from ${build.classes.dir}"/> <delete> <fileset dir="${build.classes.dir}" includes="**/*.class"/> </delete> <echo message="Deleting all classes from ${build.test.classes.dir}"/> <delete> <fileset dir="${build.test.classes.dir}" includes="**/*.class"/> </delete> </target> Also, there is sometimes a problem with badges, see issue #120585. I don't think, it would be too much work in NB to support this scenario officially. And it would save us and our customers lots of work each time we create a project.