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Alternatively to creating a classloader for the application at runtime, allow to configure at fxlauncher classloader at boot-time and add the new classpath-entries to this classloader.
This should avoid problems where the jdk itself uses Class.forName (e.g. URLStreamHandler stuff) and might not find application-classes due to using the wrong classloader.
To activate this classloader one needs to add
-Djava.system.class.loader=fxlauncher.FxlauncherClassCloader
to the fxlauncher startup.
Without this argument the current behavior is still in place.