How can I manually reorder the items under the TOC (navigation on the left)? By default, it is ordered by the title of the html files.... 01, 02.,...
Why would you want to manually reorder a ToC? Could you provide some more explanation of the setup of your R Markdown file? Are you using child documents? Why do you have multiple HTML files?
This is a duplicate to a question asked on github
Answer is in
rmd_files configuration in the documentation: https://bookdown.org/yihui/bookdown/usage.html