[Jammy2211]

Summary

In the 2026-11-04 sweep, pyauto-brain hygiene refs reported 19 dead references, and 16 of them were false positives. The scanner now retries a reference that is dead in its own repo against the places it legitimately points to, before reporting it:

• Companion workspace: a HowTo course's prose points readers to its workspace, e.g. "the workspace's scripts/interferometer/modeling.py". The pairing comes from the naming convention (HowTo<Name> to auto<name>_workspace), not a hard-coded list, so the tenant firewall stays clean. It only applies if that checkout exists.
• A sibling named on the same line: e.g. "<project>_assistant's colab/contexts.yaml".
• Folders a run creates: RUNTIME_DIRECTORIES adds files, cache, cache_root and work. They are unresolvable, not dead, just like output and dataset.
• Generated folders: notebooks is unresolvable in a checkout that doesn't commit it (generated at release).

A path that is dead in its repo and in every alternative is still a finding.

Closes #583.

Tests

• test_refs_checks_companion_workspace_and_named_sibling: references that resolve in the companion workspace or the named sibling aren't flagged, and a path dead in both still is.
• test_refs_treats_run_output_and_generated_folders_as_unresolvable.
• Control check: both new tests fail against the old scanner. pytest tests/test_hygiene_*.py gives 88 passed.
• Tenant firewall: OK. Fixtures use the made-up HowToDemo and autodemo_workspace.
• Live tree: 19 findings (16 false) before the workspace fixes, 0 now, with 282 unresolvable references still skipped.

🤖 Generated with Claude Code