add manifest to update JAR manifest but also Java:Depends

usr/share/java/igv.jar:

  Class-Path: /usr/share/java/log4j-api.jar /usr/share/java/log4j-core.jar /usr/share/java/htsjdk.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-css.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-gui-util.jar /usr/share/java/batik-gvt.jar /usr/share/java/batik-parser.jar /usr/share/java/batik-svg-dom.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-transcoder.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar /usr/share/java/commons-io.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/commons-net.jar /usr/share/java/concurrent.jar /usr/share/java/gson.jar /usr/share/java/guava.jar /usr/share/java/httpclient.jar /usr/share/java/httpcore.jar /usr/share/java/jama.jar /usr/share/java/jargs.jar /usr/share/java/jcommon.jar /usr/share/java/jfreechart.jar /usr/share/java/jhdf5.jar /usr/share/java/net.sourceforge.jlibdeps.jar /usr/share/java/junit4.jar /usr/share/java/log4j-1.2.jar /usr/share/java/sam.jar /usr/share/java/swing-layout.jar /usr/share/java/xml-apis.jar /usr/share/java/xml-apis-ext.jar /usr/share/java/AbsoluteLayout.jar /usr/share/java/bcprov.jar /usr/share/java/jgrapht0.8.jar /usr/share/java/jide-oss.jar /usr/share/java/commons-io.jar /usr/share/java/cofoja.jar