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Just want to note my progress in case someone stumbled upon this thread from google.
Using kfxlib from jhowell (can be found in KFX Output Plugin code), the YJ_Book class can be created easily with kpf input file. After decode_book() the ION can be accessed via book.fragments. To get the sense of what fragment is what the code in yj_*.py help a lot.
In the end I gave up. I first tried to just add new TOC item to the KPF book, but there seems to be multiple places where this need to be added. Futhermore, after a few hour playing with the structure, I still cannot figure which ION hold the "spine" of the book.
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