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eschwartz, I do aggree with kovid here, ... and at the beginning my opinion was like yours about the BIG importance of "folder" structure.
I mean, why are you and other people so focused on internal epub folder structure? From the final user point of view it's pretty irrelevant. Only the spine order is important.
I could understand that interest in folders in the publishing staff which where manually managing the unzipped epub, adding and deleting files, copying from other base templates,... (And on second thoughts, probably even for that people the structure is irrelevant if they use any kind of automated tool in helping them..., like Calibre Edit Book).
So currently you can:
+Fully ignore internal ebook structure as it has no visible effect.
+Manually (and manually but in bulk) modify it to your own preference.
+Automatically (but manually launched), modify it based on file types.
And you also want "Aumotatically and automatically launched". What for? Just because Sigil did?
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