[invalidname]

How did you do code callouts? Admonitions etc.?

From my experience you need to use custom syntax for those which means tooling doesn't work well. (grammar, spelling, style etc.).

O'Reilly and Manning standardized on asciidoc.

[atomicnature]

For extending markdown capabilities, there are many plugins/filters. Example [1].

I remember using extensions/filters for citations, etc.

Ultimately it is just some custom tooling around pandoc; so whatever you can do in pandoc, you can get done in the book.

[1] - https://github.com/chdemko/pandoc-latex-admonition

[2] - https://pandoc.org/