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.classpath is an eclipse thing, it has nothing to do with jar files, you need to put all your libs you use into your MANIFEST file, like this
note that the manifest needs to end in 1 blank line, why? i dont know.
Manifest-Version: 1.0 Created-By: 1.5.0 (Sun Microsystems Inc.) Main-Class: com.dogself.main Class-Path: lib/backport-util-concurrent.jar lib/bcmail-jdk14-132.jar lib/bcprov-jdk14-132.jar lib/checkstyle-all-4.2.jar lib/commons-codec-1.3.jar lib/commons-httpclient-3.0.1.jar lib/filterbuilder.jar lib/FontBox-0.1.0-dev.jar lib/highlighter-2.0.jar lib/htmlparser.jar lib/lucene-core-2.0.0.jar lib/lucene-demos-2.0.0.jar lib/PDFBox-0.7.3.jar lib/tm-extractors-0.4.jar lib/trove.jar lib/log4j-1.2.13.jar lib/commons-logging_1.0.4.jar lib/commons-logging-api_1.0.4.jar
Look for an Eclipse plugin called Fat Jar
If its compatible with your Eclipse version, you can export a whole project with all its jars with two clicks. Sometimes useful for testing, but I would say that it's better to work with individual jars and add them to the classpath.