Building a project with spring-boot-maven-plugins makes it impossible for guice to find classes using ClassPath.getTopLevelClasses()

I’m writing an application using Guice for dependency injection.
I have another 3’rd partly library (zuul2) that uses ClassPath.getTopLevelClasses() to find all the filters (if written in Java and not Gradle).

To package this I’m aiming for the spring-boot-maven-plugin to package a jar with all dependencies. It works great except that getTopLevelClasses() no longer works, the resource are now named BOOT-INF.classes.com.whatever.company.

I need to be able to configure Guice to remove BOOT-INF.classes from resource names when they are found?