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I do have epub2 book with wrong spine (files in it are also in wrong order).
I was able semi-automatically to fix correct order and create correct toc.ncx.
Each file contains one or zero chapters linked from toc.ncx, they mostly have correct title tags
It would be very difficult to do reordering manually in Calibre or Sigil(book have a lot of files) so I'm looking to automated/semiautomated solution.
How to change spine (and, preferable,order of files in epub) to be in toc.ncx order?
How to at least rename chapter files from index_<random_digits> to their real titles so manual re-ordering would be easier?
If there is no existing tools - which python libraries can be used to get access to toc.ncx and to perform reordering?
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Possible solution (which worked for me):
generate calibre's ToC(as html) from correct toc.ncx (if not arleady exist)
unpack epub
re-import only html toc,
convert result to epub
if order is incorrect yet again - check Calibre's HTML-ZIP importer depth-first/breadth first mode
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