I set out likewise to write a highly structured book with FOSS, therefore: git, some hierarchical plain text format, and a visually rich editor. Markdown could not seem to meet the third point. For instance, progress-related comments that would be stripped from final output were essential, but Markdown's HTML-style comments are intolerably unergonomic, and editors know how to de-emphasize no other syntax.

Ended up with Org-mode. Emacs with a bit of customization color- and font-codes richly. Org text goes into an Org-to-HTML converter that I hacked up in Go, incrementally added to as new wants arise.

Most recent completed production was a photo album for relatives. In HTML form, it could be put on line, but I used Weasyprint so I could give them self-contained PDF as a keepsake.