Originally Posted by user_none
FlightCrew is correct in this regard. According to the EPUB 2 spec unmanifiested files (like iTunesMetadata.plist) are to be ignored and are not considered an error.
I haven't looked at the EPUB 3 spec in a while but if I remember correctly the appearance of unmanifested files in the 3 spec were changed to have some specific requirements. Instead of ignoring them they are now supposed to be treated as an error. Again I haven't confirmed but I believe anything not in the META-INF directory needs to be manifested in 3 which it does not need to be in 2.
So what you're seeing is not FlightCrew missing something. You're seeing a difference in the EPUB 2 and 3 spec.
Hmm... OK. Just out of interest, When Sigil removes the itunes thing, is that because it is a known nuisance or does Sigil remove anything that is not manifested?