Although this is and old question, I post the solution for future reference:
It is only required to include the additional JAR files in the classpath ("-cp *" if JAR files in the same directory). Since "-cp" is incomptible with the "-jar" option, the class "net.sourceforge.plantuml.Run" should be specified.
Due to the shadowing issue, it is necessary to disable it using the "-Sshadowing=false" option.
For example, to run the GUI interface, using the PDF format ne next command can be used:
java -cp * net.sourceforge.plantuml.Run -Sshadowing=false -tpdf -gui