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These are all side effects of the evolution of calibre. Many features in current calibre did not start out that way, as a result some plugins have to adapt or their user experience becomes sub-optimal. For example, both virtual libraries and marked books are an evolution of long standing internal features of calibre that were used by find duplicates back when they were still internal. It's not find duplicates fault that those internal features have evolved, but nonetheless, it needs to evolve too.
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