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In the same way we have dependencies, we often have:
a package within a package such as a node_modules in an npm, mono-repos, uberjars and fatjars, and similar
multiple personalities for the same package (bower and npm)
We should have a heuristic to report one of these has primary and the other as sub/embedded packages.
This would likely be done in a post-scan step.
Data-wise this could be a list of Package URL similar to what we have for dependencies.