I'm not sure what you mean by "in the extracted .class file".
If you are interested in packaging your application to distribute to users, look at the Assembly plugin:
http://maven.apache.org/plugins/maven-assembly-plugin/
Actually, I have couple of jar files living at src/main/resources
You should never do that. JAR files belong in the Maven repository, not within the source of your application. If the JARs are open source, then they are probably already available in the Maven Central repository. If they are not open source, you should use the deploy:deploy-file goal to load them into your local repository. Then add them as dependencies in your pom.xml. (Alternately, you should install a Mavne repository manager such as Nexus or Artifactory, and place the JARs there.)