This forms a skeleton Bookdown production project, with an eye toward publishing via Github Pages.
First, clone the repository you want to work in, called {$REPO}. This may be a user/organization repository (organization.github.io) or a Github project gh-pages branch.
Then use composer to install the Bookdown project as a subdirectory inside {$REPO}. We suggest _bookdown since Github Pages will not publish underscore-prefixed directories.
cd {$REPO}
composer create-project -s dev bookdown/project _bookdown
cd _bookdown
Generate the example project:
./vendor/bin/bookdown book/bookdown.json
This will generate the example HTML files at the root of {$REPO}.
To browse the example HTML, run the built-in PHP server:
php -S localhost:8080 -t {$REPO}
Edit the templates/head.php file to modify the <head> on all generated files.
Edit the book/bookdown.json file to add your own book/ content, including both Markdown and other bookdown.json files.
You may wish to add the following lines to {$REPO}/.gitignore:
/_bookdown/vendor
Then git add the _bookdown/ directory along with the generated files, and push to publish.