If is possible I would like to keep the project structure even in the jar file.

...what exactly do you meant by the project structure is being changed when the jar is generated?

I meant that literally the structure of the project is being changed when I generate a jar of the project. But fortunately I was able to solve the problem minutes ago by using the following library: https://github.com/lukehutch/fast-classpath-scanner.

That's cool! Problem solved then!