I'm adding references to a Bookdown document (gitbook style) and I would like them to to appear at the end of the chapter they're cited in. No matter what I try, the rendered version of the book keeps placing them all at the end of the final chapter. Does anyone have any suggestions for how to fix this? Did I somehow screw up my split_bib = TRUE argument? Here are the configuration settings I have:

_output.yml:

bookdown::gitbook:
  css: style.css
  split_by: chapter
  split_bib: true
  config:
    sharing:
      facebook: false
      twitter: false
    toc:
      collapse: section
      scroll_highlight: true
      before: |
        <li><a href="./">Book Title</a></li>
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
bookdown::pdf_book:
  toc_appendix: true
  toc_depth: 3
  fig_width: 6.5
  documentclass: book
  classoption: oneside
  df_print: kable

_bookdown.yml:

book_filename: "file-name"
language:
  ui:
    chapter_name: ""
delete_merged_file: true
rmd_files: 
  - index.Rmd
  # A bunch of other rmd files; this part is working

Beginning of index.Rmd:

title: "title"
author: "author"
date: "`r Sys.Date()`"
description: "Description"
site: bookdown::bookdown_site
output: 
  bookdown::pdf_book
  bookdown::gitbook
bibliography: [book.bib, packages.bib]
csl: copeia.csl
link-citations: yes