[Jammy2211]

Closes #543 (phase 1 of making the Cortex the Science project manager; phase 2, cortex birth, follows as its own issue).

Summary

• New read-only pyauto-brain cortex drift [--science-root PATH] [--json] compares the laptop Science tree (<root>/<category>/<project>) with projects.yaml. The root is derived from the rows' local_paths.
• Errors (exit 1):
  • a folder in active/ or development/ with no row;
  • a non-retired row whose folder is gone;
  • a category that disagrees with the row's status;
  • a derived root that no longer exists while other rows' folders do. This is the 2026-10 incident: Science moved under Workspace\\, and pull reached 3 of 12 active projects.
• Warnings:
  • an unregistered complete/ or archive/ folder (storage);
  • a ral_root in a different category from its local_path.
• census and checkin (dry-run and apply) print a one-line summary. census() itself stays drift-free, so the board rendered in CI doesn't depend on the machine.

API Changes

None to the library API. The conductor gains a verb: cortex drift. census --json gains a top-level drift key (CLI output only, not in census()).

Review findings addressed

• A symlinked --science-root (~/Science/Science) produced false unregistered errors and skipped the category checks. Paths now compare after realpath; there's a test.
• checkin --dry-run (the default) didn't print the drift line. It does now; there's a test.
• Clearer messages for a row with no local_path and for an explicitly given root.
• Stated limit, with a test: detecting the laptop relies on some row's folder existing. The repo-backed ~/Code rows provide that today.
• Plan step 6 expected 4 warnings on the real tree; there are 11, and all are genuine: the 4 development projects, euclid and euclid_dr1 RAL categories, and 5 unregistered storage folders.

Validation

Against the real tree with PyAutoCortex#77's register: 0 errors, 11 warnings, exit 0. Against the pre-#77 register: 12 errors, exit 1.

Companion: the PyAutoCortex PR on the same branch (docs, decision 62). Land PyAutoLabs/PyAutoCortex#77 first.

Heart RED override (development only)

Authorized by the live human on 2026-10-29: "I authorize" (for PyAutoBrain#543, after the exact RED reasons were shown). Development ship only: commit, push, PR-open. Merge needs a separate human /prm with every required check green. No release.

Exact RED reasons (pyauto-heart readiness, 2026-10-29):

• PyAutoArray: 4 uncommitted source change(s)
• PyAutoGalaxy: 9 commit(s) behind origin
• PyAutoLens: 7 commit(s) behind origin
• release validation incomplete: no rehearsal for current source
• release push credential check stale (pyautolabs-bot, 49h old)

None of these involves PyAutoBrain or PyAutoCortex. This branch does not fix them.

Passed branch gates: Brain tests/test_cortex_conductor.py 71 passed (12 new); Cortex cortex check: OK + 65 tests; no new ruff findings; no smoke leg applies (no workspace or library code); independent review FINDINGS, all addressed (see below).

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