How to fix "WARN: Quarto did not expect the path configuration being used..." warning in project with separate src/ and docs/ directories?

[rogilmore]

Description

My typical Quarto project has separate src/ and docs/ directories under the project root directory. I render via the command line using quarto render src. The src/_quarto.yml file sets output-dir: ../docs.

This all worked splendidly until I upgraded to RStudio 2025.9.1.401 (Mac OS Sequoia 15.7.1; Quarto 1.8.24) a few weeks ago. Now, the HTML output files render to docs/, but I get warning/error messages like this:

WARN: Refusing to remove directory ../my_project_root/docs/site_libs since it is not a subdirectory of the main project directory.

Any thoughts about what has changed? I like my project structure because it separates the source files from the output, but the warnings are annoying. Happy to keep ignoring them if this is a known bug that's in the queue.

I note that #2171 touches on related issues, but that was before the output-dir yaml parameter was implemented, I believe.

[mcanouil]

The warning is there to make it clear what is happening and is new (1.8), but the behaviour itself is not new.
This usage goes agains Quarto's design to have self-contained projects.
Here Quarto is "finally" telling you that it can't and won't cleanup a directory outside the project (too high risk of doing something wrong).

If you don't want the warning then conform with the design by setting output-dir to a directory within the project (where _quarto.yml lives) and define a post-render script that copies/moves the directory elsewhere.