I am not at my pc right now to review your changes and what I call but I would guess my open with plugin uses both of those, and it intentionally wants to work with write access to the original files in place.
Suggestions? Edit in Sigil and resizing covers are continual tasks I and many other users take advantage of. I would hate to have to put a tweak ePub type of dialog up where the user is blocked from doing other actions in calibre while editing.
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