I just finished building an reproducible environment for another bookdown ebook. This time the turn for a complex book on Bayesian Statistics by A. Solomon Kurz (link:https://github.com/ASKurz/Statistical_Rethinking_with_brms_ggplot2_and_the_tidyverse)
Now, the ebook, with its dependencies, can be reproduced easier. I used rsuite to build the control project on top of the bookdown project. Repo to book project statistical_rethinking-rsuite here: https://github.com/f0nzie/statistical_rethinking-rsuite.
I have found rsuite is great for creating complex reproducible environments.