chore: canonical organ order — Eyes after Memory, before Heart (pyautoeyes-birth)

[Jammy2211]

Overview

Phase 0 of pyautoeyes-birth (PyAutoMind#437) placed PyAutoEyes after Gut in every organ list. The human ruled on 2026-09-25 that the canonical organ order is Brain, Mind, Cortex, Memory, Eyes, Heart, Hands, Nerves, Gut: Eyes goes after Memory and before Heart. This task moves Eyes to that position in every hand-maintained list and regenerates every generated block. Nothing changes except the order.

Plan

• Move the Eyes row in the Mind body map (repos.yaml) and the session-start hook chains to sit between Memory and Heart.
• Reorder the hand-maintained sibling-organ lists and organ prose in Brain, Heart, Hands and the hub page.
• Regenerate every generated block (map blocks, organ tables, Scientist README, root routing table) with repos_sync.py --write.
• Hand-edit the unversioned organs/AGENTS.md. The .github org-profile table stays a human edit.
• Witness: repos_sync.py --check passes the organism-map and organ-table legs with Eyes between Memory and Heart. A grep of SIBLING_ORGANS in Brain, Heart and Hands shows the same order.

Detailed implementation plan

Affected Repositories

• PyAutoMind (primary)
• PyAutoBrain, PyAutoHeart, PyAutoHands, pyautolabs.github.io, PyAutoScientist, PyAutoCortex, PyAutoNerves, PyAutoGut

Branch Survey

Repository	Current Branch	Dirty?
./PyAutoMind	main	clean
./PyAutoBrain	main	clean
./PyAutoHeart	main	clean
./PyAutoHands	main	clean
./pyautolabs.github.io	main	clean
./PyAutoScientist	main	clean
./PyAutoCortex	claude/checkin-2026-09-19	dirty (7 science-ledger files from another session; the task worktree branches off origin/main)
./PyAutoNerves	main	clean
./PyAutoGut	main	clean

Suggested branch: feature/eyes-organ-order
Worktree: ~/Code/PyAutoLabs-wt/eyes-organ-order/

Implementation Steps

1. PyAutoMind: move the PyAutoEyes row in repos.yaml so it sits after PyAutoMemory and before PyAutoHeart. Reorder the directory chains in policy/session_start_hook.sh.
2. PyAutoBrain: reorder agents/_pyauto_root.py SIBLING_ORGANS and bin/_pyauto_root.sh. Also reorder the ORGANISM.md organ table, docs/concepts/organism.md, the docs/index.md toctree and the README.md organ list.
3. PyAutoHeart: reorder heart/_workspace.py and heart/_workspace.sh.
4. PyAutoHands: reorder autohands/_workspace.py.
5. pyautolabs.github.io: reorder the index.html organism blurb.
6. Run python3 PyAutoMind/scripts/repos_sync.py --write to regenerate the map blocks in Brain, Cortex, Nerves and Gut AGENTS.md, the Scientist README and the root routing table. The .github org-profile table is a human edit.
7. Hand-edit organs/AGENTS.md. It is an unversioned root file, so tar a backup first.
8. Verify: repos_sync.py --check (the hub-blurb leg is already red on main, and hook propagation may lag), then pytest for Brain, Heart and Hands.
9. Note for phase 2: the policy.yaml boards and _theme.py must use the new order when they land.

Key Files

• PyAutoMind/repos.yaml: the body map, which is the source of every generated block
• PyAutoBrain/agents/_pyauto_root.py, PyAutoHeart/heart/_workspace.py, PyAutoHands/autohands/_workspace.py: the SIBLING_ORGANS lists
• PyAutoBrain/ORGANISM.md: the organ table

Original Prompt

Click to expand starting prompt

Canonical organ order — Eyes after Memory, before Heart

Type: maintenance
Target: PyAutoEyes
Repos:

• PyAutoMind
• PyAutoBrain
• PyAutoHeart
• PyAutoHands
• pyautolabs.github.io
• PyAutoScientist
• PyAutoCortex
• PyAutoNerves
• PyAutoGut
  Difficulty: small
  Autonomy: supervised
  Priority: high
  Lane: local-dev
  Status: draft
  Witness: python3 PyAutoMind/scripts/repos_sync.py --check organism-map/organ-table legs OK with Eyes between Memory and Heart in every generated block; grep of SIBLING_ORGANS lists in Brain/Heart/Hands shows the same order.
  Epic: pyautoeyes-birth
  Filed: 2026-09-25

Request (verbatim)

I just applied the patch, but I dont think Eyes belong after Gut, I think
they belong after Memory before Heart which should be the canonical order

Context

Phase 0 of pyautoeyes-birth (complete/2026/09/pyautoeyes-birth-organ-row.md,
PyAutoMind#437) appended Eyes after Gut everywhere. The human ruled on
2026-09-25 that the canonical organ order is:

Brain, Mind, Cortex, Memory, Eyes, Heart, Hands, Nerves, Gut

Files to reorder (the phase-0 touch list)

• PyAutoMind: repos.yaml (move the Eyes row between Memory and Heart);
  policy/session_start_hook.sh directory chains.
• PyAutoBrain: agents/_pyauto_root.py SIBLING_ORGANS;
  bin/_pyauto_root.sh; the ORGANISM.md table; docs/concepts/organism.md;
  the docs/index.md toctree; the README.md organ list.
• PyAutoHeart: heart/_workspace.py and heart/_workspace.sh.
• PyAutoHands: autohands/_workspace.py.
• pyautolabs.github.io: the index.html blurb.
• Then run repos_sync.py --write to regenerate the map blocks (Brain, Cortex,
  Nerves and Gut AGENTS.md), the Scientist README and the root routing table.
  The .github org-profile table is a human edit.
• The organs/AGENTS.md root file is unversioned, so edit it by hand.

Note for later phases

The phase-2 items (the policy.yaml boards and _theme.py) must use the new
order when they land.

[Jammy2211]

Checkpoint 2026-09-25 (session ended at bedtime; resume from here)

State: reorder implemented and gated, committed in 8 repos on feature/eyes-organ-order in bundle ~/Code/PyAutoLabs-wt/eyes-organ-order/ — nothing pushed, no PRs open.

Repo	Commit
PyAutoMind	569fce85 (repos.yaml row moved Memory→Eyes→Heart; hook chains rewritten in canonical order; ORGANS cosmetic)
PyAutoBrain	639c316 (SIBLING_ORGANS, _pyauto_root.sh, ORGANISM.md, docs, README, regenerated AGENTS.md)
PyAutoHeart	8e177ca (_SIBLING_ORGANS, _workspace.sh, config/repos.yaml organism group)
PyAutoHands	c0aa50d
PyAutoCortex f4979a1 · PyAutoNerves 71542c7 · PyAutoGut d523e89e	regenerated map blocks
PyAutoScientist	dfa965a (regenerated organ table)
pyautolabs.github.io	no diff needed (blurb already in order)

Gates: Mind pytest 585, Brain 1002 + docs 0 warnings, Heart 1035, Hands 463, Cortex 63, Nerves 185; ruff clean; repos_sync --check OK except .github table (human), hub blurb (pre-existing), hook copies (propagate after Mind merge).

Heart at checkpoint: YELLOW (score 70, no RED reasons): workspace validation 4 failed (cloud#35579888156); manifest drift hub-blurb 7 / organism-map 1 / workspace checkouts 1; release validation stale (source moved since rehearsal).

Resume: (1) human acknowledges the YELLOW set (or override if RED again) naming this task; (2) push + open the 8 PRs — bodies in <bundle>/tmp/handover/pr_bodies_order/ (fill <AUTHORIZATION QUOTE>); merge order Mind first, then the rest (Brain's pytest reads the Mind body map — expect a re-run after the Mind merge as in #437); (3) human applies <bundle>/tmp/handover/order_spill/.github.patch (one-row organ-table move) — the earlier hand-applied .github row must sit between Memory and Heart; (4) /prm close-out. Root AGENTS.md routing table already regenerated locally (unversioned). Then phase 1: draft/feature/pyautoeyes/eyes_p1_repo_restructure_skeleton.md.

[Jammy2211]

Parallel claim note: workspace-config-cleanup (PyAutoMind#441) also claims PyAutoNerves, on branch feature/workspace-config-cleanup in its own worktree. It touches only scripts/board.py and its tests. This task's Nerves diff is only AGENTS.md, so there is no overlap. The human approved this on 2026-09-27.

[Jammy2211]

Parallel claim (human-approved 2026-09-27): where-to-file-block (PyAutoMind#442) also claims PyAutoMind and PyAutoBrain on feature/where-to-file-block. Disjoint from eyes-organ-order (#439): #439 touches Mind repos.yaml organ order, the two hook copies and the 4-line _repo_resolver hunk in scripts/repos_sync.py, plus Brain agents/_pyauto_root.py, bin/_pyauto_root.sh, docs/. #442 touches only repos_sync.py block constants/new functions/main wiring, policy/, tests/, skills/create_issue, .github/workflows/session_hook_propagate.yml and Brain skills/intake/.

[Jammy2211]

Parallel claim (human-approved 2026-09-28): autolens-visualization-rebirth (PyAutoMind#446, PyAutoEyes phase 1a) also claims PyAutoMind, PyAutoBrain and PyAutoHeart on feature/autolens-visualization-rebirth, in its own worktree. The only overlap with eyes-organ-order (#439) is Mind repos.yaml: #439 reorders the organ rows, while #446 adds a project row (autolens_visualization) after autolens_inference and rewrites the PyAutoEyes role string. #446 also touches Mind ROUTING.md, Brain agents/conductors/eyes/AGENTS.md, skills/eyes/eyes.md and bin/clean_slate.sh, and Heart config/repos.yaml. Whichever PR merges second rebases its repos.yaml hunk and re-runs repos_sync --write.

[Jammy2211]

Parallel claim on PyAutoBrain (human-approved 2026-09-28): task eyes-organ-skeleton (#448, PyAutoEyes phase 1b) branches feature/eyes-organ-skeleton in PyAutoBrain. There is no file overlap: it touches only tests/test_policy_seams.py and config/policy.yaml (moving PyAutoEyes from WITNESS_EXEMPT to a test_witness row).

[Jammy2211]

PRs created

Canonical organ order (Brain, Mind, Cortex, Memory, Eyes, Heart, Hands, Nerves, Gut) — every branch rebased onto its current origin/main on 2026-09-28 (all clean), one commit each. Merge is human; merge Mind first, the rest in any order.

1. PyAutoMind — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) #449
2. PyAutoBrain — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoBrain#427
3. PyAutoHeart — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoHeart#241
4. PyAutoHands — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoHands#291
5. PyAutoCortex — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoCortex#46
6. PyAutoNerves — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoNerves#177
7. PyAutoGut — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoGut#13
8. PyAutoScientist — chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoScientist#35

pyautolabs.github.io has no diff, so it gets no PR.

Heart: YELLOW (score 65, no RED). The human acknowledged this exact yellow set in-session on 2026-09-28 (it is recorded as heart-ack in active.md).

Validation: Mind 618 passed, Brain 1078, Cortex 64, Nerves 209, Gut 23, Scientist 8. Heart has 1062 passed and 1 failed. Hands has 471 passed and 1 failed. The failing test in both is test_the_family_footer_carries_the_cortex_in_the_canonical_order, and it already fails on main (Heart Tests on a95ebc9; Hands reproduced on an origin/main worktree). The cause: Brain main added the Nerves and Gut boards (PyAutoNerves#172, PyAutoGut#9) but these tests still expect the old list. This task does not cause that failure and does not fix it.

Overlap with #446: PyAutoMind#447 rewrites the PyAutoEyes role strings, and #449 moves that same block. Whichever PR merges second needs a rebase that keeps #447's strings at #449's position. Heart#240 does not overlap with Heart#241.

Human-only: the one-row .github/profile/README.md organ-order edit. The patch is at the workspace root, tmp/handover/order-dotgithub.patch.

[Jammy2211]

Shipped — closed via /prm

The canonical organ order is now Brain, Mind, Cortex, Memory, Eyes, Heart, Hands, Nerves, Gut across the organism. All eight PRs were merged by the human on 2026-09-28:

• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) #449 — repos.yaml Eyes row moved between Memory and Heart; policy/session_start_hook.sh directory chains
• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoBrain#427 — SIBLING_ORGANS, _pyauto_root.sh, ORGANISM.md, docs organism/index, README
• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoHeart#241 — heart/_workspace.py / _workspace.sh
• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoHands#291 — autohands/_workspace.py
• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoCortex#46, chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoNerves#177, chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoGut#13 — regenerated organism-map blocks
• chore: canonical organ order — Eyes after Memory, before Heart (PyAutoMind#439) PyAutoScientist#35 — regenerated README organ list

pyautolabs.github.io had no diff after rebase onto main, so there was no PR.

Human-only work still to do. The .github org-profile README cannot be edited by an agent. The patches are kept at tmp/handover/eyes-organ-order/order-dotgithub.patch (the Eyes row order) and tmp/handover/eyes-organ-order/map-block-dotgithub-post449.patch (the map block after #447 and #449). Both paths are relative to the workspace root.

Hook propagation. The #449 merge push did not trigger session_hook_propagate, so it was started by hand with workflow_dispatch as run 36479476721. The run concluded failure. It pushed the regenerated session-start.sh to every other in-scope repo, but the push to PyAutoCortex was rejected (fetch first) because PyAutoCortex#47 merged at the same moment. PyAutoCortex main still holds the previous hook copy, so a re-dispatch of the workflow is needed to bring it level.

Pending release: all eight PRs carry pending-release, and these lines are carried into the completion record.