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It's too complicated to setup a SIMPLE project in NetBeans, compared to Eclipse. For example, when creating a new J2SE project, the option for the destination directory of the compiled .class files is missing. So you could specify to have them created into the source directory, just like the default in NB 3.x. Of course a rule in build.xml for deleting those .class files when cleaning has to be added, too. For example: <target name="-post-clean" depends="init"> <echo message="Deleting all classes from ${build.classes.dir}"/> <delete> <fileset dir="${build.classes.dir}" includes="**/*.class"/> </delete> </target>