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As for the time to delete the now merged resources, it takes a long time because it requires parsing the opf, updating the manifest, spine, guide, and any nav landmarks (so parsing and recreating the nav each time too), then rebuilding the opf and saving it each time repeated for over 100 resources.
Only the merge case would require deleting so many resources at once, so it was designed for single use and safety not speed. I will look into adding a bulk removal routine to save some time.
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