`output-dir` mirrors source folder structure instead of placing HTML directly in target folder

RStudio IDE
,
1

Hi all,

I'm using Quarto (1.8.25) with RStudio on Windows 11 and having an issue with output-dir not behaving as expected.

My project structure is:

.
├── 0-info
├── 1-data
│ ├── cohort_list1.xlsx
│ └── DATA_2026-04-20_1047.csv
├── 2-programs
│ ├── 01_create_cohort_list.qmd
│ └── Missing Forms.qmd
├── 3-results
│ └── 2-programs
│ └── Missing Forms.html
├── Missing Forms.Rproj
└── _quarto.yml

My _quarto.yml:

project:
  type: default
  output-dir: "3-results"

Expected behavior: HTML output goes directly into 3-results/

Actual behavior: Quarto mirrors the source folder structure and places the output at 3-results/2-programs/Missing Forms.html instead of 3-results/Missing Forms.html

I have tried execute-dir: project and various ../ combinations in output-dir without success.

Any help appreciated. Thanks!

RStudio version:

RStudio 2026.01.1+403 "Apple Blossom" Release (0e924abb984501b0d66b204ea06b60fc7813275a, 2026-02-04) for windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2026.01.1+403 Chrome/140.0.7339.249 Electron/38.7.2 Safari/537.36, Quarto 1.8.25