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I just came across this thread. Some tips:
1) Do not use the INDX entries to build an NCX. INDX entries can have a maximum depth of two for books and 3 for periodicals. This is a limitation of the MOBI format. Instead parse the inline TOC, calculate the left indents and reconstruct the NCX from that. See code in mob/reader.py in calibre to do that.
2) If you still want to decompile indx entries and are looking at calibre code to figure out index entries:
a) note that currently indexer.py does not generate depth 2 indx entries for books, primarily because I got tired figuring out the TBS indexing for depth to book nodes.
b) you should look at the code in mobi/debug.py which is designed to decompile arbitrary MOBI files including the index and TBS information. You can run that code with calibre-debug --inspect-mobi filename.mobi
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