quarto has different `.Rprofile` behavior in Single File mode depending if `--output-dir` is used

I have:

• 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 the --execute-dir <dir1> option R will be launched from the target directory <dir1> thus using the .Rprofile of that directory, this is regardless of where the source file lives.

However if you also provide --output-dir <dir2> R will instead be launched from the directory of the source file thus ignoring any .Rprofile file in <dir1> or <dir2>. I'm not 100% sure but I think in this case you are launching R from the source file directory and then internally running setwd() to move the directory to <dir1>. This issue occurs even if <dir1> and <dir2> are the same directory.

Steps to reproduce

> tree -a        
.
├── .Rprofile
├── code
│   └── test2.qmd
└── runme.sh

.Rprofile

cat("hi from code/.Rprofile\n")
cat("getwd() = ", getwd(), "\n")

test2.qmd

---
title: "Untitled"
format: html
---


```{r}
getwd()
```

runeme.sh

quarto render \
  code/test2.qmd \
  --execute-dir $(pwd) \
  --metadata "embed-resources: true"


quarto render \
  code/test2.qmd \
  --output-dir "$(pwd)" \
  --execute-dir "$(pwd)" \
  --metadata "embed-resources: true"

Actual behavior

The first render attempt (just using --execute-dir) makes use of the .Rprofile and produces stdout of:

> quarto render \
  code/test2.qmd \
  --execute-dir $(pwd) \
  --metadata "embed-resources: true"
hi from .Rprofile
getwd() =  /Users/gowercr1/Desktop/Work/xxx-testing-quarto 


processing file: test2.qmd
1/3                  
2/3 [unnamed-chunk-1]
3/3                  
output file: test2.knit.md

The second render however does not load the .Rprofile

> quarto render \
  code/test2.qmd \
  --output-dir "$(pwd)" \
  --execute-dir "$(pwd)" \
  --metadata "embed-resources: true"


processing file: test2.qmd
1/3                  
2/3 [unnamed-chunk-1]
3/3                  
output file: test2.knit.md

Expected behavior

Both should use the .Rprofile from the execution directory

Your environment

MacOS - 26.6.2
R version 4.6.1 (2026-06-24) -- "Happy Hop"

quarto --version
1.10.18

Quarto check output

> quarto check           
Quarto 1.10.18
[✓] Checking environment information...
      Quarto cache location: /Users/gowercr1/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.10.0: OK
      Dart Sass version 1.101.0: OK
      Deno version 2.7.14: OK
      Typst version 0.15.1: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.10.18
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chrome Headless Shell: (not installed)
      VeraPDF: (not installed)

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /Library/TeX/texbin
      Version: 2026

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
      Source: MacOS known location

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

[✓] Checking R installation...........OK
      Version: 4.6.1
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.6/Resources/library
      knitr: 1.51
      rmarkdown: 2.32

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

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

[✓] Checking Julia installation...

Start by reproducing the two quarto render commands with --execute-dir and with both --execute-dir and --output-dir, then trace the CLI's Single File execution-directory handling. Compare how R is launched in each case and verify that both commands load the .Rprofile from the execution directory when done.