FWIW, you aren't converting the JAR into an ALX file, but rather the COD file (assuming that's what you're doing here). The ALX file would be similar to a JAD file or the Manifest file found within a standard JAR. It's simply an XML-based installation instructions file that is parsed for correct information for Application Loader to install the actual installation files (COD, etc). The COD file, by definition, is obfuscated JAR file.
Just some clarification.