I agree that, theoretically, an unindexed file in the <manifest> "does not exist" in the ePub, and that therefore technically the ePub is broken.
But not really either because the files are well used (in the <link> and <img>), but their
non-importation breaks the ePub
even more.
Problems that could have been fixed become unfixable.
Is a conversion problem, possible. But the idea is that not everyone is also respectful of the standard, so a little caution will be good.
The most vicious thing is that sometimes some files are indexed, others are not.
I am not asking for a systematic addition but just a check, which can be done using the "file table" of the ZIP archive. And no need to decompress any files, just load the OPF in memory and read the entries of the <manifest> (if Sigil was in C#, I could tried it).
Then Sigil works normally, and creates a conforme ePubs.
If it proves too complex to implement, okay, very sad, but I just want to reported this problem and ask for some thought to solve it.
To answer KevinH: So you ask me to 1) open with a "ZIP opener" each ePub I want to work 2) looked in the OPF the correspondence <manifest> contained in the ZIP 3) added the entries "forgotten" ? By hand?
This is possible, but the goal of a software is it to automate tedious, repetitive and sometimes complex tasks? Might as well take advantage of it.