It is widely known (see How to delete Calibre ePub bookmarks), though not to my knowledge documented, that Calibre makes modifications to EPUB documents even without the user's choosing to edit them.

The best-known among these modifications is the insertion of a file named calibre_bookmarks.txt into the META-INF/ directory.

Does the application make any other modifications in this context?

I see the word calibre in style names in various CSS files in EPUB documents that also contain the bookmarks. Is this structure more likely to result from surreptitious editing of the document by the reader application, or is it more likely to result from the document originally being created by the Calibre editor?

Asked differently, if given an EPUB document, how might one comprehensively test whether the Calibre reader had made modifications to the .epub file subsequent to it being originally published by the author?

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