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Eclipse has a "Fat Jar" plugin that can create a jar containing your classes/resources and all classes/resources from all dependencies.
Technically it's possible to do this from command prompt but...

First: it has no sense (and it's useless) that you put external jars into your jar. The JVM will not search jars into your jar!


It's not correct that the jar contains the 'classes' directory. If...

External jars must be declared into the manifest. The manifest should have a line like:

Class-Path: lib/other1.jar lib/other2.jar

The "lib" sub folder is just an example. Other jars must be...