Lua filter not applied to bibliography in HTML output for multi-page books

Bug description

When rendering a Quarto book project to HTML, I've encountered an issue where a Lua filter (citation-backlinks.lua) is not applied to the bibliography if the bibliography is rendered in a separate references.qmd file as follows:

# References {.unnumbered}

::: {#refs}
:::

This behavior is observed when the project includes a references.qmd file, which moves the bibliography list from the index.html to references.html. The Lua filter is intended to add citation backlinks to the bibliography entries.

This issue does not occur when rendering the book to PDF or DOCX formats, which suggests that the problem might be related to how Quarto processes and applies Lua filters in the context of generating multi-page HTML outputs. In PDF and DOCX formats, the output is self-contained, and the Lua filter is applied successfully to the bibliography.

Steps to reproduce

1. Create a Quarto book project with the following structure in _quarto.yml:

project:
  type: book
  output-dir: _book
book:
  title: Lua Filter Test in Quarto
  chapters:
    - index.qmd
    - references.qmd
bibliography: bib.bib
csl: gb-author-date.csl
format:
  html: default
  docx: default
  pdf: default

2. Use the command quarto render --to html -L _extensions/citation-backlinks/citation-backlinks.lua to render the project to HTML.
3. Observe that the Lua filter is not applied to the bibliography in references.html.

You can also view the full demo project here.

Expected behavior

The Lua filter should be applied to the bibliography in all output formats, including when the bibliography is rendered in a separate HTML file (references.html) for multi-page book projects.

Actual behavior

The Lua filter is applied successfully in PDF and DOCX outputs but not in the HTML output when the bibliography is rendered in references.html.

Your environment

• IDE: VS Code
• OS: macOS Sonoma 14.5

Quarto check output

$ quarto check

Quarto 1.5.52
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.52
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.06
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/user/Library/TinyTeX/bin/universal-darwin
      Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.10
      Path: /Users/user/.pyenv/versions/3.10.10/bin/python3
      Jupyter: 5.7.2
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.4.1
      Path: /opt/homebrew/Cellar/r/4.4.1/lib/R
      LibPaths:
        - /Users/user/.R/packages
        - /opt/homebrew/lib/R/4.4/site-library
        - /opt/homebrew/Cellar/r/4.4.1/lib/R/library
      knitr: 1.47
      rmarkdown: 2.27

[✓] Checking Knitr engine render......OK

Start by reproducing the command quarto render --to html -L _extensions/citation-backlinks/citation-backlinks.lua with the _quarto.yml and references.qmd structure described, then compare the HTML result with PDF and DOCX output. Trace how multi-page HTML books process the bibliography and invoke the Lua filter; done means citation backlinks appear in references.html.