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Help with a possible issue with ePub Structure

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Ok first of all here is my situation:
I am using the Calibre plugin Fanfic Fare to download fanfiction.net stories and I am using Cool Reader 3 to open them on my PC and my iPhone.

My issue is this:
Cr3 can not use the Table of Contents and can not navigate the chapters unless Calibre creates an inline TOC as part of the downloaded epub. That Table of contents is a series of links at the start of the epub and not the actual TOC

A work around I have found is this:
I have downloaded Sigil and now I open a epub using Sigil, I save the epub (just that, I do not edit it) and the end result has a fully functioning TOC.

I checked to see if I could find out what might be the issue and I changed the extention of both the epubs to zip and found that the folder structure is different.

Specifically:
1) in the OEBPS folder in the original epub there is no Styles or Text subfolders and the files that should have been inside those folders are all in the OEBPS folder.
2) the content.opf and toc.ncx files are in the "root" directory in the original while in the edited they are in the OEBPS folder.

Note: Obviously the content.opf and toc.ncx are edited by Sigil in order to show the new location of the files in the updated file structure

There might be other differences but I don't know a way to check, the above is just obvious
I have added the original epub and an edited result if you want an example to check

What I would like to find out:
Some kind of explanation about the difference between the 2 versions of the epub. That way I could search for some quicker way to do the above conversion.
Right know what I do is: after the download is complete I open the folder the epub is downloaded to, then I open the epub with Sigil, save the opened file, quit Sigil and then open the File using Cr3.
The current problem is that Sigil does not have command line options like:
sigil --save --and-then-quit "filename.epub"
that I could use as a shortcut or in a bat file so that I could do the all of the above with 1 or 2 clicks, and maybe use a command line like that for batch conversion of multiple epubs.

The reason I want the above explanation is that if I at least know some kind of fundametal difference between the 2 epubs (like for example if one of them was lets say epub v2 instead of epub v3) I could search for some other program that would do the same faster and easier (and as I said maybe that program could be run through the command line:D).
However all epub checkers I have found either just say that both epubs are ok or tell me the same results:smack:

Could you help me out:help:
Thanks you:thanks:


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