Cross-reference link to chapter file in a book works in HTML but not in PDF

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• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

When using a cross-reference link to a chapter [chapter](chapter.qmd), the link does not work correctly in PDF. That is, it end up being an \href{chapter.qmd}, instead of \ref{chapter} in the generated LaTeX. This is at odds with the documentation, which states that

Using the source file as the link target ensures that links will be resolved correctly both for HTML output and for formats that produce a single file (e.g. PDF or MS Word).

Steps to reproduce

index.qmd:

# Preface {.unnumbered}

This is a Quarto book.

To learn more about Quarto books visit <https://quarto.org/docs/books>.

Using a simple link to [the introduction file](intro.qmd) does *not* work in PDF, but an explicit cross-reference using [the reference](#sec-intro) does work.

intro.qmd

# Introduction {#sec-intro}

This is a book created from markdown and executable code.

See @knuth84 for additional discussion of literate programming.

_quarto.yml

project:
  type: book

book:
  title: "Test cross-references"
  author: "Norah Jones"
  date: "8/27/2025"
  chapters:
    - index.qmd
    - intro.qmd

format:
  pdf:
    keep-tex: true

Actual behavior

The link [the introduction file](intro.qmd) is translated into \href{intro.qmd} in the generated LaTeX. This in turns lead to a hyperlink in the PDF to the qmd file, not to the chapter in the generated PDF.

Expected behavior

It should generate LaTex that does something like \hyperref[sec-intro], as it does when using the explicit reference [the reference](#sec-intro). That way, it leads to a hyperlink within the PDF.

Your environment

• OS: Linux freedom 6.14.0-27-generic #27~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 22 17:38:49 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
• VScode: 1.102.0

Quarto check output

Quarto 1.7.33
[✓] Checking environment information...
      Quarto cache location: /home/vtraag/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.85.1: OK
      Deno version 1.46.3: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.33
      Path: /opt/quarto/bin

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

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /usr/local/texlive/2024/bin/x86_64-linux
      Version: 2024

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/google-chrome
      Source: PATH

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.3
      Path: /usr/bin/python3
      Jupyter: 5.3.2
      Kernels: python3

(|) Checking Jupyter engine render....Traceback (most recent call last):
  File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/opt/quarto/share/jupyter/notebook.py", line 20, in <module>
    from nbclient import NotebookClient
ModuleNotFoundError: No module named 'nbclient'
[✓] Checking Jupyter engine render....OK

Start by rendering the sample book from index.qmd, intro.qmd, and _quarto.yml to PDF with keep-tex enabled. Compare the generated LaTeX for the intro.qmd link with the explicit cross-reference, and confirm that the source-file link resolves to the chapter anchor rather than the qmd file.