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Please check the specifications of the ePUB3 format on the IDPF site or look at the wiki of Mobileread.
The folder structure has not changed from ePUB2 to ePUB3.
There are no real editors for ePUB3 as of yet, so it is all manual work. I have heard that the latest ID can save as ePUB3, but I am not sure about the quality.
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