Fixed commons-cli version number as well as added missing runtime dependencies
Fixed commons-cli version number as well as added missing runtime dependencies

iliat/dataflow-java,deflaux/dataflow-java,nitag/dataflow-java,deflaux/dataflow-java,deflaux/dataflow-java-OBSOLETE,deflaux/dataflow-java-OBSOLETE,iliat/dataflow-java,jakeakopp/dataflow-java,nitag/dataflow-java,jakeakopp/dataflow-java,googlegenomics/dataflow-java,googlegenomics/dataflow-java,deflaux/dataflow-java,googlegenomics/dataflow-java