fix: hygiene refs flags companion-workspace and run-output paths as dead #583

Overview

In the 2026-11-04 sweep, pyauto-brain hygiene refs reported 19 dead references, and only 3 were real (fixed in autolens_workspace#621). The other 16 resolve, but against a root the scanner doesn't try:

• Companion-workspace paths in HowTo prose: e.g. HowToLens says "The workspace's scripts/interferometer/modeling.py", which lives in autolens_workspace.
• A sibling repo named on the same line: the autocti_workspace README names autocti_assistant's colab/contexts.yaml.
• Folders a run creates: files/search_internal is fit output, autoreduce's work/injected/, cache_root/crds/ and README cache are run data, and notebooks is only generated at release in autoreduce_workspace.

Plan

• If a reference doesn't resolve in its own repo, try the paired workspace of a HowTo repo (HowToLens to autolens_workspace, HowToGalaxy to autogalaxy_workspace, HowToFit to autofit_workspace).
• Also try any sibling repo named on the same line as the reference.
• Treat files, cache, cache_root and work as run-produced folders, like output and dataset.
• Treat notebooks as generated when the repo has no notebooks/ folder, so the reference can't be checked.
• Add fixture tests for each class, and keep the existing dead-reference tests passing.
• Done when the laptop scan reports 0 of these 16, and a genuinely dead path in a HowTo repo is still flagged.
• Tier: glance — merge mode: human /prm