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Some day maybe. But that design decision is truly embedded in Sigil from day 1 (or close to it). Sigil depends on and enforces that model and as such each xhtml file must be correctly parseable, etc so that links can be updated. The movement of files to a standard structure should do no "harm". If an epub passes epubcheck and is loaded into Sigil, it should (in its new layout) pass epubcheck. If not that is a bug and I will track it down and fix it.
All that said, once BV has been dealt with, and missing epub3 fixed-layout support has been added, I will look into making the relayout an option only.
But that will not happen for quite a while yet.
Sorry,
Kevin
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