Idea for consideration:

Not sure how much time Windup spends on comparing package prefixes (or rather, retrieving them from the storage), but we could build a package tree in the graph when scanning, and when looking for classes from given package org.foo.*, we could select with Gremlin:
PackageModel[name=org] – contains --> PackageModel[name=foo] – contains --> JavaClassModel .loop()
That could be faster when the numbers of classes in the projects get to hundreds of thousands.