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What you and some others aren't understanding is that it's not as simple as just "pop a warning when things don't match." In order to warn a user that an unmanifested file exists when opening/saving, Sigil would first have to KNOW there's an unmanifested file when opening/saving. And I can assure you that it does not. And MAKING sigil aware would require an overhaul of the open/save process that is simply not in the cards right now. Sorry. Patches welcome, though. I'll happily code the warning if someone provides the rest.
Sigil isn't deliberately deleting unmanifested files, it's simply failing to SAVE a file it doesn't know exists--couldn't possibly know exists without a double-parsing of the epub (opf manifest and internal archive file list) and file-by-file comparison of the two each and every time an epub is opened/saved. I'm not interested in tackling that.
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