Take your time, I do not think I will have time to work on this before next week.
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SMIL files position: I have no preference, and it makes sense for Sigil to move the .smil files into OEBPS/Smil/ for consistency with the other type of assets.
(Currently, I put the .smil files of my EPUB3 in the OEBPS/Text/ directory, along with the .xhtml files. But the specs does not mandate a specific position for them. With respect to reading systems, there is no drawback choosing one internal location over another. Those supporting Media Overlays do it in a "spec compliant" way, NOT relying on naming conventions like expecting the smil files in say OEBPS/Text/ or similar.)
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