Title: DOCX output truncates after the first footnote when using specific CSL and PDF cite-method settings

[hhkosar]

Description

I am writing my doctoral dissertation using Quarto (v1.x) and I am facing a critical issue with the .docx output. While my project renders correctly in PDF (using biblatex), the Word output behaves unexpectedly.

The Problem:

Content Truncation: When rendering to docx, the resulting document is truncated immediately after the first footnote. The rest of the document text and subsequent footnotes are missing from the generated file.

YAML Conflict: There seems to be a conflict when defining cite-method: biblatex for PDF and trying to use a CSL-based workflow for DOCX in the same _quarto.yml.

Implicit Mapping Errors: Even with a clean YAML, Quarto occasionally throws YAMLException: can not read an implicit mapping pair when both formats are defined, particularly around citation-related keys.

Steps to reproduce: I am using a book project with the following structure:

index.qmd

chapters/*.qmd

My _quarto.yml configuration:

---
project:
  type: book
  output-dir: _book

bibliography: references.bib
csl: university-style.csl

format:
  docx:
    reference-doc: template.docx
    toc: true
  pdf:
    pdf-engine: xelatex
    cite-method: biblatex
    include-in-header:
      text: |
        \usepackage{tocloft}
        \setlength{\cftbeforechapskip}{2.5em}

Expected behavior: The docx output should render the entire manuscript with all footnotes processed according to the CSL file, regardless of the PDF cite-method settings.

Actual behavior: The docx file is generated but stops abruptly after the first footnote citation. No error message is provided during the render process to indicate why the content is being truncated.

Environment:

**OS:** Linux/Ubuntu

**Quarto Version:** 1.8.26

**Pandoc Version:** 3.1.3

[mcanouil]

Carefully read the log message.
You've placed csl as a global option, thus it applies to all formats including LaTeX.
The message is telling you that it conflicts, thus move csl to where it's needed, which seems to be under docx.

For more help, see below.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.