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I'm attaching a PDF of a book with inserted highlights and notes to this post along with associated files to make it. It turns out that the utility html2ps does not choke on the XML in a rawml file like my web browser does, so there was no need to comment out the XML. What is also surprising to me is that the TOC in the PDF works. This is not meant to be a book with highlights and notes, but rather the highlights and notes shown in context.
The source book is EPUB of The Humbugs of the World by P T Barnum from the Mobileread Library. I used kindlegen to make a dual mobi and used kindleunpack to extract the rawml and azw3, which I copied to a kindle and quickly made 9 highlights with bogus notes.
Then I copied the azw3r and dumped the notes, which also gives the start and end of the each higlight. Next I used the notes_insert.pl from the first post to modify the rawml, then html2ps and ps2pdf. You can search the PDF for '[HL]' or '[Note:' to find the highlights and notes.
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