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SQL Developer does provide command line support for some UI features like Unit Testing and Formatting (look in the sqldeveloper\bin directory for the scripts), but not unfortunately for the Refactoring feature. That is available only from the UI.
SQL Developer Team
Thanks for the response. I hope it's a feature that could find it's way in, in a future release.
I believe the command line interface is getting some updates in the next release, but I don't see refactoring or obfuscation on the list of features that will be supported. You may want to add that as a new feature request on the SQL Developer exchange.