: Re: Is there an ebook format that stores annotations in the ebook file itself? I believe .epub and .mobi files both don't support annotations. Which is unfortunate since they are some of the most

@Ashley

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The KDE linux program Okular has the ability to store annotations inside PDF files:

By default, Okular saves annotations in the local data directory for each user. Since KDE 4.9, it's optionally possible to store them directly in a PDF file by choosing "File -> Save As...", so they can be seen in other PDF viewers.
Note that this feature requires Poppler 0.20 or newer for regular PDF documents. If the PDF document you are annotating is encrypted, this feature requires Poppler 0.22 or newer.

It also has the ability to archive a document along with metadata (i.e. annotations) into an Okular-specific archive format:

Since KDE 4.2, Okular has the "document archiving" feature. This is an Okular-specific format for carrying the document plus various metadata related to it (currently only annotations).
You can save a "document archive" from the open document by choosing "File -> Export As -> Document Archive".
To open an Okular document archive, just open it with Okular as it would be eg a PDF document.

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