index_files not copied to project.output-dir with certain markdown formats

Bug description

Hi folks.

I am rendering a document with project.output-dir specified in _quarto.yml

When some index.qmd contains a code block to generate some index_files, the index_files directory is not being copied to the output-dir when certain output formats (like hugo-md) are used.
The index_files are correctly copied with other output formats (like pdf or commonmark), so this is somehow format-specific.

Steps to reproduce

note: this example was edited to reflect advice below about project.type = hugo

The code below replicates the issue for me on the following quarto version:

quarto --version

shows 1.6.40.

First let's make a .qmd that we will use.
I am using a small mermaid diagram as a code chunk that should generate dependencies in index_files.
We put in page sub-directory.

mkdir ./page
echo -e "---\ntitle: my title\n---\n\n\`\`\`{mermaid}\nflowchart LR\nA[start] --> B[end]\n\`\`\`" > page/index.qmd

I will then use _quarto.yml files to vary the render behavior.
We save the output to output sub-directory.

md output behaves, as I understand, correctly.

echo "project:\n    output-dir: output\nformat: md" > _quarto.yml
quarto render page/index.qmd
ls output/page

The ls output shows:

index.html      index_files

Here is an example with gfm output.

# gfm
rm -rf ./output
echo "project:\n    output-dir: output\nformat: gfm" > _quarto.yml
quarto render page/index.qmd
ls output/page

and now the ls command only shows index.md.

And here is an example with hugo-md which also sets project.type to hugo.

rm -rf ./output
echo "project:\n    output-dir: output\n    type: hugo\nformat: hugo-md" > _quarto.yml
quarto render page/index.qmd
ls output/page

again ls only shows index.md

Expected behavior

As I understand, we should always expect index_files to appear in the output dir.

Actual behavior

On my side, the following outputs place index_files in the output-dir:

• pdf
• typst
• html
• md
• markdown
• hugo-markdown
• commonmark
• hugo-commonmark

And these formats do not plaace index_files in the output dir:

• hugo-md
• gfm
• hugo-gfm

and that's all I have tested.

Your environment

• OS: MacOS Sonoma 14.5
• quarto 1.6.40 installed as homebrew cask

Quarto check output

quarto check   

Quarto 1.6.40
[✓] Checking environment information...
      Quarto cache location: /Users/michaeldecrescenzo/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.6.40
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.12
      Chromium: (not installed)

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

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

[✓] Checking Python 3 installation....OK
      Version: 3.13.0
      Path: /opt/homebrew/opt/python@3.13/bin/python3.13
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.3.3
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: (None)
      rmarkdown: (None)

      The knitr package is not available in this R installation.
      Install with install.packages("knitr")
      The rmarkdown package is not available in this R installation.
      Install with install.packages("rmarkdown")

Reproduce the issue with page/index.qmd and the three _quarto.yml configurations, especially gfm and hugo-md, using quarto render. Compare the generated output/page contents across formats and trace the format-specific output handling. Done means index_files is copied into output/page for the affected formats without regressing the formats that already work.