`quarto render` calls that produce `.md` should ignore that `.md` file in additional renders

Bug description

In a simple default project (a) Quarto file/s have format: gfm (github flavored markdown). Rendering each file individually only create an .md file, as it should. If none of the files have been rendered, a global project render via quarto render only generates .md files. However, if a .md file already exists, quarto render also creates an html file output.

Steps to reproduce

Create a temporary directory and enter it, create a basic default Quarto project and a minimal .qmd file with gfm format; render the project for the first time:

temp_dir=$(mktemp -d) && cd $temp_dir

echo 'project:
  title: "tmp"' > _quarto.yml

echo '---
title: "Index"
format: gfm
---' > index.qmd

quarto render
ls -l

Output:

pandoc 
  to: >-
    commonmark+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars
  output-file: index.md
  standalone: true
  default-image-extension: png
  
metadata
  title: Index
  
Output created: index.md

-rw-r--r--  1 vpopov  staff  24 Dec  2 13:56 _quarto.yml
-rw-r--r--  1 vpopov  staff  10 Dec  2 13:56 index.md
-rw-r--r--  1 vpopov  staff  35 Dec  2 13:56 index.qmd

Render again:

quarto render
ls -l

Output:

[1/2] index.qmd
[2/2] index.md

Output created: index.html

total 64
-rw-r--r--  1 vpopov  staff     24 Dec  2 13:56 _quarto.yml
-rw-r--r--  1 vpopov  staff  17084 Dec  2 13:56 index.html
-rw-r--r--  1 vpopov  staff     10 Dec  2 13:56 index.md
-rw-r--r--  1 vpopov  staff     35 Dec  2 13:56 index.qmd
drwxr-xr-x  3 vpopov  staff     96 Dec  2 13:56 index_files

Expected behavior

Create all and only the formats specified in yaml headers, either in project settings or notebook settings; Consistently render the same type of output regardless of state of the filesystem.

Actual behavior

In a simple default project (a) Quarto file/s have format: gfm (github flavored markdown). Rendering each file individually only create an .md file, as it should. If none of the files have been rendered, a global project render via quarto render only generates .md files. However, if a .md file already exists, quarto render also creates an html file output.

Your environment

• IDE: zsh terminal
• MacOS 15.2

Quarto check output

Quarto 1.6.39
[✓] Checking environment information...
Quarto cache location: /Users/vpopov/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: 1.6.39
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: v2024.05
Chromium: 869685

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

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

[✓] Checking Python 3 installation....OK
Version: 3.12.1 (Conda)
Path: /opt/miniconda3/bin/python
Jupyter: 5.5.0
Kernels: ir, python3

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

[✓] Checking R installation...........OK
Version: 4.4.2
Path: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources
LibPaths:
- /Users/vpopov/Library/R/arm64/4.4/library
- /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
knitr: 1.48
rmarkdown: 2.28

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