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Then enable full book paths in BookBrowser via Preferences so it will always show full paths (or just mouseover without that preference set).
There is no true standard layout for epub2 or epub3. The old Sigil "standard" layout is and was a horrible kludge and harsh limitation for an an epub editor that forced file relocations on opening that did end up breaking things like javascripts and etc.
We will not be bringing it back.
If you build epubs from scratch you can create a template empty epub that matches the layout you want using Sigil empty layout tools.
If you open an existing epub, you open it with the layout as set by the original epub developer.
If you do not like that layout, you can use Sigil to move folders and files where you like or use the menu tool to make it like the old forced layout.
None of this will be changing.
That said, point me to broken plugin code and I am sure that I and others can fix them so that they work with any layout. That is how Sigil should have been from the very beginning.
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