Since JDeveloper 12c it’s possible to uninstall extension from your JDeveloper, without deleting jar files and cache directories manually. However, the feature is a little bit hidden, it’s not in your preferences, but in the feature section. You get there through the Tools menu.
Now if you go to the second tab, installed updates, you get an overview of the updates installed on your JDeveloper.
If you tick for example JUnit, JDeveloper is also smart enough to recognize the dependency. It warns you that you need to uninstall both the bundles.
Next you can click the uninstall button and restart JDeveloper.
That's all it takes to uninstall an extension in JDeveloper 12c.