Job run via REST erases "pipeline.classpaths" config

The JarHandlerContext#applyToConfiguration creates a PackagedProgram and then overwrites the pipeline.jars and pipeline.classpaths values according to that newly created PackagedProgram.

Although that PackagedProgram init does not set classpaths at all, so it will always overwrites the effective configuration with an empty value, even if it had something previously.