_bookdown.yml

# this sets the directory that your output gets stored in
# Putting it in a 'docs' folder is convenient if you want to publish HTML
# output with GitHub Pages 
output_dir: "docs"

# If the below is set to true, you don't have to manually delete the merged 
# _main.Rmd file if something goes wrong when you try to build
delete_merged_file: true

# By default, bookdown will automatically merge .Rmd files in the root folder
# into your thesis. If you specify a sub directory with rmd_subdir, bookdown
# searches through this folder too. .Rmd files you don't want automatically
# included, should start with an underscore, e.g. _abstract.Rmd (otherwise 
# bookdown would merge the abstract into the body text)
rmd_subdir: ["front-and-back-matter"]

# You can override bookdown's automatic merging of files, and explicitly
# specify files to include with "rmd_files" like this:
#rmd_files: ["index.Rmd", "01-rmd-basics-markdown.Rmd", "02-rmd-basics-code.Rmd", "03-rmd-basics-cites-and-refs.Rmd", "04-oxthesis.Rmd", "05-conclusion.Rmd", "front-and-back-matter/98-appendices.Rmd", "front-and-back-matter/99-references.Rmd"]

# If you want people to be able to suggest and submit changes to the source .Rmd
# files on your github repo, do it like so (https://bookdown.org/yihui/bookdown/html.html)
edit: https://github.com/ulyngs/oxforddown/tree/master/%s