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OK, just found a solution, thanks to @cedricbatailler. The problem came from the "_" prefix in my "_notes/docs", which seems to be interpreted by Github Pages / Jekyll as "do not build this file" (e.g., https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/about-github-pages-and-jekyll).

Two solutions: either remove the "_" prefix in "docs/notes" (after rendering the website with Quarto) or (the solution I went for) output the bookdown gitbook directly in a folder at the root of the Quarto website in a folder that does not contain a "" prefix, such as "notes", then adding this folder to the resources in _quarto.yml (as I have done here: https://github.com/lnalborczyk…

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