The error indicates that you don't have all of the required libraries (in the lib directory) on the classpath. I can't speak to the MatLab-specific aspect. The manifest in the NetLogo.jar should add all of the libs in the lib directory to the classpath, assuming NetLogo.jar and the lib directory are in the same location in the filesystem. But if you're having trouble getting the manifest to handle it for you, a workaround you could try would be to explicitly put all of the jars under lib on the classpath yourself.
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