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Any move or rename or splitting or merging of anything will invoke the update all links code. This code was always run from the beginning. In the old Sigil the added the folder to the path was a workaround instead of resolving the simplest relative path.
So your version of the link from epub root we be would be the following:
OEBPS/Text/../Text/notes.xhtml
which would then need to be simplified.
whereas in current Sigil the link destination will be built as
OEBPS/Text/notes.xhtml
with no further simplification needed.
So if you stop making any changes to the epub or mending of code, no changes will be made to links. But once a file name is changed or a mend is done, a split is done, etc, the links will be corrected and properly updated, just as Sigil always has done.
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