(we crossed paths in the bitstream)
So if the kindlegensrc.zip is supposedly the source files, it is not the exact source files: the directory structure is modified, and the files are tweaked to reflect the changed directory structure.
Maybe exporting any unknown binary data into files would make disassembling it a bit easier, at least. I have no clue where the .ncx file goes, or what format it gets placed in (maybe Kovid does), but without any obvious way of looking at it, it is pretty hard to figure that out. Seems reasonably likely, if there are more binary pieces than mobiunpack presently ignores, that one (or more) of them probably is the .ncx data.
And maybe others would be the .mp3 files I was asking about earlier, although sadly adding .mp3 files is something that keeps slipping further out in my project list.
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