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I noticed the section numbers in generated output did not match the text or input files. This is fixed by enabling pandoc attributes and making the preface unnumbered.
Also the internal links were all broken. Fixed by using header identifiers.
Note I couldn't get github to run the actions for me so I've only tested the pandoc changes locally with a version that may or may not match the version used on github.
There's still at least one broken link, chapter 12's matmul.k. I'll leave it to you to decide how to fix but I guess for pdf & epub users, simply using an absolute URL would work best.
I found a few more typos too.