There is a critical problem with package discovery when running the application in source mode.
Git clone this application to recreate the problem.
https://github.com/ivargrimstad/jakartaee-duke
Try analyzing the application in source mode specifying the path to jakartaee-duke
The package discovery does not discover the packages within the java files, within the subfolders. Rather the package names presented are the names of the 2 sub-folders

• complete-duke
• transformer-duke

Those 'package names' are passed through to the analysis. Obviously no classes match those packages so the class based rules don't fire.

• If you specify the input as the path to jakartaee-duke/complete-duke the package discovery correctly identifies eu as a package and the class based rules fire.