`output-file` with `.html` extension loses the markdown-format output in multi-format project renders (website render fails at move step)

[cscheid]

Bug description

In a project render that pairs format: html with a markdown format (e.g. commonmark, as in llms.txt workflows), setting output-file to a name with an .html extension (e.g. output-file: index.html, which nbdev sets on every page it generates) breaks the render of the markdown twin:

• Website project: quarto render fails with a hard error at the output-move step — it tries to move <name>.html.md from the project root into _site, but the file was never written. The already-rendered index.html and site_libs/ are left stranded in the project root.
• Default project: quarto render exits 0, but the markdown output is silently missing — no .md file is produced anywhere. Presumably the same underlying bug with a quieter symptom.

Notes from narrowing this down:

• output-file: index (no extension) works correctly in both project types (_site/index.html + _site/index.md).
• Not index-specific: output-file: other.html on a non-index page fails identically.
• Rendering a single file/format works: quarto render index.qmd --to commonmark correctly produces _site/index.html.md (so the collision-avoiding <name>.html.md naming itself works; it's the multi-format project render that loses the file).
• Reproduces identically with released 1.9.38 and current main dev build (8577ed1).
• Related history: the reporter of quarto-nav.js's index.html clean-URL rewrite mangles alternate-format links on index pages #14667 observed on 1.8.25 that this config routed site_libs and the .md twin outside _site, so some form of this misbehavior is longstanding. (Found while reproducing quarto-nav.js's index.html clean-URL rewrite mangles alternate-format links on index pages #14667, which needs this config to exercise its client-side bug end-to-end.)

Steps to reproduce

_quarto.yml:

project:
  type: website

format:
  html: default
  commonmark: default

index.qmd:

---
title: Home
output-file: index.html
---

Hello.

Then:

quarto render

Actual behavior

ERROR: NotFound: No such file or directory (os error 2): rename '<project>/index.html.md' -> '<project>/_site/index.html.md'

Stack trace:
    at Object.renameSync (ext:deno_fs/30_fs.js:267:3)
    at safeMoveSync (file:///.../src/deno_ral/fs.ts:102:10)
    at renderProject (file:///.../src/command/render/project.ts:526:9)

After the failed render, index.html and site_libs/ sit in the project root instead of _site, and no index.html.md exists anywhere (watching the directory during the render confirms it is never created).

With project: type: default instead: exit code 0, index.html is produced, and the commonmark output silently does not exist.

Expected behavior

The render succeeds and produces _site/index.html and _site/index.html.md, matching what the single-format render (quarto render index.qmd --to commonmark) already produces.

Your environment

• macOS 26.x (Darwin 25.5.0), arm64
• Reproduced with Quarto 1.9.38 (release) and quarto-cli main @ 8577ed1 (dev build)

Quarto check output

Dev build at 8577ed1; quarto check unremarkable (Pandoc 3.8.3, Deno 2.4.5).