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The Yellowfin installer is a java archive (.jar) file. This is essentially a zip-compatible file, with some special properties. The Java Development Kit comes with a command-line tool for creating and extracting these files, called
jar.exe on Windows).
jar cvmf META-INF/MANIFEST.MF /path/to/yellowfin-modified.jar *
This command creates a new installer jar file, using the contents of the original file and any additional files you have added. The jar manifest file from the original installer is used.
See http://launch4j.sourceforge.net/ for more information.