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					Originally Posted by GERGE  I know that Calibre doesn't support ePub 3 files, because of that I always modify them by hand.
 But how well can I use plugins like Modify ePub, and Calibre's built-in tools like polishing and conversation tools?
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GERGE - I don't think you can use those tools, or any others that deal with the internal data of the EPUB3 formats.  See this recent thread for some relevant discussion ==>> 
Signalling needed properties for EPUB3
Its up to the 'owners' of optional PI's like Modify to develop EPUB3 versions of the plugins.
BR