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While it is certainly possible to create endnotes as internal html links. I was wondering if the ePUB committee has or will address the need for an ePUB footnote. They talk about allowing the application to code it but they don't provide any unique way for an application to know it is a footnote and not some other kind of link. I would think a new tag would be appropriate such as the wiki uses. <ref>this is a footnote</ref> would automatically be enough to code in a footnote and then the reading application would use that data to generate a proper footnote, or even an endnote depending on what the application could do.
Dale
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