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Frequently Asked Questions
The covers aren't mandatory, but without them things like the cover grid and carousel are somewhat boring to look at. You can delete covers en masse in bulk metadata edit. If you do that then you might want to consider what you're going to do if/when you change your mind and want 'em back again.
The metadata.opf files are mandatory, even if you delete them calibre will recreate them - leave them alone.
Why are you worrying about them anyway? Many here will argue that you shouldn't even be looking at the content of the library folders - I don't go that far - but I do say 'look but don't touch'.
If you want covers and metadata embedded in the book files then use the Embed metadata feature. More than a few users specifically want keep their original files in the library and metadata/covers adjusted ones on their devices. Send to device will send the book with the library cover and metadata embedded.
BR