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Why is the last "for" loop in the "do while"? It seems to me that removalPending never changes and therefore this could be put outside of the "do while". The first "for" in the "do while" could be made faster by remembering the initial size of the graph, so on the next iteration it goes from graph.size() to previous size instead of going to 0.
The code has undergone major changes. PackageAdminImpl no longer computes affected bundles. This is all handled by the State.