Hi Ephemerality, I've had some great success with you tool. After a bit of help though.
I'm converting my epubs to AZW3 for use on my Paperwhite (1st generation) and every book I run through XRay Builder does not generate the 'chapters' part of the entities file. Perhaps it has something to do with my conversion settings in Calibre or what is in the RAWML file. Here's the relevant section from the RAWML file (I think).
Spoiler:
<?xml version="1.0" encoding="UTF-8"?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Table of Contents</title>
<link href="kindle:flow:0003?mime=text/css" rel="stylesheet" type="text/css"/>
</head>
<body id="calibre_generated_inline_toc" aid="1AT9A0">
</body>
</html>
<h2 aid="1AT9A1">Table of Contents</h2>
<ul aid="1AT9A2">
<li aid="1AT9A3"><a href="kindle
os:fid:0000
ff:0000000000" aid="1AT9A4">Dedication</a></li>
<li aid="1AT9A5"><a href="kindle
os:fid:0001
ff:0000000000" aid="1AT9A6">Chapter 1</a></li>
<li aid="1AT9A7"><a href="kindle
os:fid:0002
ff:0000000000" aid="1AT9A8">Chapter 2</a></li>
<li aid="1AT9A9"><a href="kindle
os:fid:0006
ff:0000000000" aid="1AT9AA">Chapter 3</a></li>
<li aid="1AT9AB"><a href="kindle
os:fid:0009
ff:0000000000" aid="1AT9AC">Chapter 4</a></li>
<li aid="1AT9AD"><a href="kindle
os:fid:000D
ff:0000000000" aid="1AT9AE">Chapter 5</a></li>