There is no way to have absolute path urls for internal epub files.
If the source xhtml is in Text/ and uses a relative href "../Text/notes.xhtml", that url is simplified to notes.xhtml since that is the correct destination. The "../Text" is unneeded and does in no way clarify the link destination.
So when Sigil went 1.0, it allowed for users to have any organization they want for their epub and the need and use for prefacing a destination with its folder went away since those links can now be relative to other folders and need not be correct anymore.
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