Scheduled smoke tests always fail due to env var pollution from editor-support crossref test

The weekly scheduled run of test-smokes.yml (sequential mode, no buckets) has been failing consistently for 3+ months — every single run fails with the same 36 tests. Meanwhile, the parallel bucketed runs (test-smokes-parallel.yml) pass 100%.

Recent examples:

• Sequential (fails): https://github.com/quarto-dev/quarto-cli/actions/runs/23131055254
• Parallel (passes): https://github.com/quarto-dev/quarto-cli/actions/runs/23134392459

Root cause

In sequential mode, all smoke-all tests run in the same Deno process. The editor-support-crossref test for tests/docs/smoke-all/2023/10/17/issue-7259.qmd triggers src/command/editor-support/crossref.ts, which sets a process-wide environment variable that is never cleared:

https://github.com/quarto-dev/quarto-cli/blob/5b88d3dfe1519179e2e8753c44e058a11ab62ff3/src/command/editor-support/crossref.ts#L91-L92

Once QUARTO_CROSSREF_INPUT_TYPE=qmd persists in the environment, the Lua crossref filter's isQmdInput() returns true for all subsequent renders. This causes writeKeysIndex() to run instead of writeFullIndex(), producing crossref index files without a headings field. Book post-render then crashes at book-crossrefs.ts:263 with:

TypeError: Cannot read properties of undefined (reading 'forEach')

In parallel mode, each bucket runs on a separate GitHub Actions runner (separate VM), so the env var pollution cannot cross bucket boundaries.

Failing tests (36 total, identical on Ubuntu and Windows)

All book-type project tests that run after issue-7259.qmd in alphabetical order:

• docs/smoke-all/2024/02/01/issue-8514/ (book)
• docs/smoke-all/2024/02/22/8814/ (book)
• docs/smoke-all/2024/12/12/11520/ (book)
• docs/smoke-all/2025/12/10/13769/ (book)
• docs/smoke-all/2026/02/24/issue-12136/ (book)
• docs/smoke-all/book/page-footer/ (book)
• docs/smoke-all/book/simple/ (book)
• docs/smoke-all/brand/logo/*-book/ (book)
• Plus a few listing and engine class-override tests (likely related shared state issues)

Related

#12621 addresses the broader Deno.env.set cleanup (milestoned for v1.10). A targeted fix for this specific leak could unblock the scheduled CI sooner — either clearing the env var after use in editor-support/crossref.ts, or making book-crossrefs.ts:263 defensive against missing headings.