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Note how the publisher organizes their files vs my own organization. My boss ~specifically~ wants all assets to be top-level. His reason for such standards is making the authoring process easier if I were to link various images. Usually, publishers would not put an 'up one level' semantic (.. in HTML) on their web pages to ease managing assets. I would understand if there is a separate folder for images, scripts, etc but are separate folders really necessary for stylesheets and web pages?
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I guess I just don't understand how having assets at the same level (top or otherwise) would have any bearing on the ease/difficulty of the authoring process. Especially since almost any authoring software in existence is going to invisibly manage those levels for you. If you want/need that kind of control over the ePub's architecture, then manually constructing them would seem to make the most sense.
In order for
any authoring software to make ePub construction "easier" (and by easier, I mean creating/managing links and handling all the recursive renaming/relinking when files get renamed, inserted, deleted... TOC building—generally the things that make authoring software attractive in the first place), the first thing it's probably going to need to do is to take absolute control over the internal structure... it wouldn't be able to do all the things that are so "handy" (in a programmatic manner) otherwise.
As to why Sigil needs to put each type of asset into its own folder; I say why not? It complies with spec and doesn't make creating/editing ePubs with Sigil any more or less difficult. One of the main reasons for using ePub authoring software in the first place is because you don't want to concern yourself with the internal, structural, nitty-gritty details, right?
I'm not certain why you're under the impression that major publishers have some sort archetypal ePub structure, anyway. In my experience, I get wildly varying internal structures in ePubs purchased from major publishers. Many of them varying wildly within the same publisher. Anything from a perfectly flat structure, to Sigil's subfolder approach. And more and more lately... an actual Sigil-built ePub.
Want control over structure?... build by hand.
Want to use authoring software?... forget about structure.
As far as lack of ePub3 support... join the crowd. Spec-compliant ePub3 authoring software is going to be just about as rare as devices that actually support spec-compliant v3 ePubs.