I have an external jar file(have package structure), which contains the main class, and I can run the app from command line like this:
java -jar example.jar
If the class is in bin directory :
java -cp xxx.jar;bin pck1.pck2.MainClass
If the class is in the current directory :
java -cp xxx.jar;. pck1.pck2.MainClass
and so on...
More info in the manual, please read it at least one time... ;-)