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The way the JARs will be added are container dependent: for example, on a Tomcat local container with a standalone configuration, the JARs are copied in the $CATALINA_BASE/lib/common folder, on a similar Jetty configuration it is added to the extraClasspath attribute of the context.xml files, etc. If you absolutely need the JARs to be added to the JVM classpath (for example, because you are changing the Java logger and it needs additional JARs), you can add the -classpath (or -cp) argument as a JVM argument in the container configuration.
Note that some containers also support adding custom JARs to the applications' classpath only: see Application Classpath for details.
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