I'm glad you figured out how to use the Polish books feature. The response below is for others that may follow.
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Originally Posted by strongnc21
Correct me if I'm wrong, but it seems to me that Calibre preserve the original ePub that you import. Any "metadata" changes aren't actually applied to the ebook file (I'm using ePub for all of my books). Instead, a book cover is stored in the same directory as the eBook (eg, .jpg), and the metadata is actually sotred in a ".opf" file.
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The metadata for all of your books is actually stored in the metadata.db file. The individual opf files you see in the directories contain info (yes metadata) for use in disaster recovery to restore the library (metadata.db) in case of corruption.
In addition to the separate cover being used to update the book it is used in displaying the calibre library via the GUI.
Quote:
Originally Posted by strongnc21
My question is, is there any way to ditch the separate metadata and separate cover files, and write that data directly to the ePub file? That way, everything is contained within the single file?
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No because as described above those files are used for other purposes within calibre.
However, please note that with epub files whenever a book is exported from the calibre library the metadata and cover are updated in the book. So if you used the Send to device, Save to disk, email to, features or obtained the book via the content server the epub should have the cover and metadata you see in calibre embedded into the epub.
Folks that ask for the books in the library to be updated are usually grabbing the book directly from the library folder instead of exporting the book via calibre's many sanctioned methods. Typically this occurs when folks use cloud sync software like Dropbox on their device to grab the books as they need them. In this use case the user would have to use the Polish books feature to embed the cover and metadata into the library copy of the book.
Quote:
Originally Posted by strongnc21
Is it a file type issue? Should I not be using ePub? That seems odd though, if you use Calibre to "explode" an ebook, there is definitely a cover file inside of it, and probably the metadata too, I have to assume...
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Personally I think ePub is the best choice. Many of the books may have a cover and metadata embedded in them as any time you convert a book the cover and metadata are embedded during the conversion process.