Hi! I'm new to gradle and have started a new gradle project in eclipse. It gives me a lib folder, and a gradle folder, but not an app-folder. I cannot find anywhere in the new-project-wizard that I want a java application, and I havn't found an easy way to create my java application there

It sounds like the the application plugin is what you're looking for https://docs.gradle.org/current/userguide/application_plugin.html If you tell it where your main class is, it'll bundle your application into a distribution and generate files for starting it

As your question is more about how to use Buildship, the Gradle integration into Eclipse, you might have more luck asking in the forum in the Buildship category. I have no idea how many poor souls that are doomed to use Eclipse are following here. :-D In that forum category afaik also the Buildship dev reads along. (cc. @Donát Csikós)