Cortex phase 0: birth — organ row, boundary prose, hub blurb

[Jammy2211]

Overview

Phase 0 of the cortex-birth epic (ledger: draft/feature/pyautocortex/cortex_birth_epic.md). On 2026-09-01 the human decided to split science runs out of PyAutoMind into a new organ, PyAutoCortex — a run/ruling-native registry: the Mind decides what to build, the Brain routes the work, the Cortex learns what is true. Phase 0 is the birth: the human creates the empty GitHub repo, and the organism's wiring is updated so the repo is an organ — body-map row, boundary prose, organ doc page, hub blurb, regenerated organ maps. Everything inside the Cortex repo itself is phase 1.

Plan

• Human creates PyAutoLabs/PyAutoCortex (public, empty). It is not cloned locally during this phase, so repos_sync --write cannot pre-empt phase 1 by installing hooks into it.
• Add the PyAutoCortex organ row to PyAutoMind/repos.yaml and regenerate every organ map and public organ table with repos_sync.py --write.
• Write the boundary prose in PyAutoBrain/ORGANISM.md (eighth organ; ruling-of-record rule), the docs/organs/cortex.md page, and fix organ counts.
• Keep Brain's tests green on the new row (WITNESS_EXEMPT, SIBLING_ORGANS).
• Add "Cortex" to the pyautolabs.github.io organism blurb so check_hub_blurb passes.
• Deviation from the prompt (approved): no _theme.py palette/mark, no policy.yaml boards: row, no install.sh edits in this phase — Gut and Nerves have none either, a board key without a palette fails test_board_theme.py, and a mark needs a logo. Phase 2 adds them with the board; phase 1 revisits install.sh.

Detailed implementation plan

Affected Repositories

• PyAutoMind (primary — body map)
• PyAutoBrain (ORGANISM.md, docs, tests, regenerated AGENTS.md map block)
• PyAutoGut, PyAutoNerves (regenerated AGENTS.md map block only)
• .github (org profile README organ table, regenerated)
• PyAutoScientist (README organ table, regenerated)
• pyautolabs.github.io (index.html blurb)

Branch Survey

Repository	Current Branch	Dirty?
./PyAutoMind	main	clean
./PyAutoBrain	main	clean
./PyAutoGut	main	clean
./PyAutoNerves	main	clean
./.github	main	clean
./PyAutoScientist	main	clean
./pyautolabs.github.io	main	clean

Suggested branch: feature/cortex-birth-organ-row (worktree root ~/Code/PyAutoLabs-wt/cortex-birth-organ-row/)

Implementation Steps

1. PyAutoMind/repos.yaml: append after PyAutoNerves —
   PyAutoCortex: {github: PyAutoLabs/PyAutoCortex, category: organ, organ: Cortex, role: "The Cortex — where the organism learns what is true: the science body map (projects.yaml) and the rulings of record for every science run; the science mirror of the Mind (runs and rulings, not prompts and PRs).", public_role: "Holds the science body map and the rulings of record for every science run, so experiments, their gates and their verdicts live apart from software development."}
2. python3 scripts/repos_sync.py --write --root <worktree-root> from the Mind worktree. Regenerates the organ map blocks in PyAutoBrain / PyAutoGut / PyAutoNerves AGENTS.md, the public organ tables in .github/profile/README.md and PyAutoScientist/README.md, and the worktree-root AGENTS.md (not a repo; canonical root copy regenerated post-merge). Absent Cortex checkout → skipped (absent).
3. Amend the phase-0 prompt in active/: step 5 deferred (theme/board/install → phase 2 / phase 1); record the repo-creation date.
4. PyAutoBrain/ORGANISM.md: organ table row after Nerves — Cortex | PyAutoCortex | learns what is true: the science body map and the rulings of record; the science mirror of the Mind (runs and rulings ↔ prompts and PRs); the Mind decides, the Brain routes and executes nothing, the Cortex learns what is true; a verdict recorded only outside the Cortex does not exist; the eighth organ. Growth-rule paragraph: one sentence naming the Cortex as the second organ that earned it (owns state no organ owned). PyAutoBrain/README.md:66-67: seven organs → eight, add Cortex (learning).
5. PyAutoBrain/docs/organs/cortex.md in the register of docs/organs/gut.md (what it owns, repo link, defining function: pre-registered witness → run → ruling, driver split with the phase-2 cortex conductor, ruling-of-record rule, gates as GitHub refs, "for an adopter": instance organ, link to the epic ledger); add organs/cortex to the toctree in docs/index.md.
6. PyAutoBrain/tests/test_policy_seams.py WITNESS_EXEMPT: add "PyAutoCortex": "born empty 2026-09-01 (cortex-birth phase 0); phase 1 adds tests/ and the test_witness row".
7. PyAutoBrain/agents/_pyauto_root.py SIBLING_ORGANS: add "PyAutoCortex".
8. pyautolabs.github.io/index.html (~:249-251): "Mind, Brain, Heart, Hands, Memory, Gut and Nerves" → "…, Gut, Nerves and Cortex".
9. PyAutoGut / PyAutoNerves / .github / PyAutoScientist: commit only the regenerated hunk.
10. Seven PRs, all doc/config. Merge PyAutoMind first, then the rest. Post-merge: repos_sync.py --write from the canonical root; /prm close-out.

Verification

• python3 PyAutoMind/scripts/repos_sync.py --check --root <worktree-root> exits 0 with the Cortex row (the prompt's witness).
• grep -l PyAutoCortex over PyAutoBrain/AGENTS.md PyAutoGut/AGENTS.md PyAutoNerves/AGENTS.md .github/profile/README.md PyAutoScientist/README.md lists all five.
• PyAutoBrain: pytest tests/test_policy_seams.py tests/test_board_theme.py tests/test_workspace_root.py -q; pyauto-brain board renders.
• PyAutoMind: pytest tests -q; lifecycle.py check OK; intake --check dashboard clean.
• Watch, not block: branch_sweep_all.yml / brain_board.yml now enumerate an empty repo (both catch clone failures with a warning).

Key Files

• PyAutoMind/repos.yaml — the body map; the organ row is the birth certificate
• PyAutoMind/scripts/repos_sync.py — routing_table, system_map, organ_public_table, check_hub_blurb
• PyAutoBrain/ORGANISM.md — organ table + growth rule
• PyAutoBrain/docs/organs/gut.md — register model for cortex.md
• PyAutoBrain/tests/test_policy_seams.py, PyAutoBrain/agents/_pyauto_root.py
• pyautolabs.github.io/index.html — organism blurb

Original Prompt

Click to expand starting prompt

Cortex phase 0 — birth: the repo, the body-map row, the boundary prose

Type: feature
Target: pyautocortex
Repos:

• PyAutoMind
• PyAutoBrain
• PyAutoScientist
• pyautolabs.github.io
  Themes:
• mind-workflow
• docs-hub
  Difficulty: medium
  Autonomy: supervised
  Priority: high
  Status: draft
  Consequence: judge
  Witness: python3 PyAutoMind/scripts/repos_sync.py --check exits 0 with a Cortex row; every organ's AGENTS.md map block lists PyAutoCortex; pyautolabs.github.io hub blurb check passes
  Review-minutes: 15
  Unattended: never
  Epic: cortex-birth
  Phase: 0
  Parent: draft/feature/pyautocortex/cortex_birth_epic.md
  Filed: 2026-09-01

Phase 0 of 7 in the PyAutoCortex birth epic. Gates nothing external; gated by
nothing. Gates phase 1 (the skeleton needs a repo to land in).

The repo is created by the human. Nothing in the organism creates PyAutoLabs
org repos (checked 2026-08-26: the only gh repo create calls make a visiting
scientist's own repo; spawn.py force-syncs into templates that already exist).
So the first act is a human one on github.com, and everything else in this phase
is the wiring that makes a repo an organ.

Context

PyAutoBrain/ORGANISM.md:63-72: "A new organ costs an AGENTS.md, a
CLAUDE.md stub, install wiring, a body-map row and boundary prose — it must
earn that by owning state or effects no existing organ can." The Cortex earns
it by owning the science body map and the rulings ledger (epic ledger, "The
decision"). The mechanical consequences of a category: organ row are known:
repos_sync.py:227-249 writes the system map into every organ's AGENTS.md
block, :265-303 regenerates .github/profile/README.md and
PyAutoScientist/README.md, :702-712 requires the name in
pyautolabs.github.io/index.html.

Task

1. Human step, first: create PyAutoLabs/PyAutoCortex on github.com
   (public — the Mind is public and the Cortex holds rulings, not data; the
   science projects it points at are the private ones). Default branch
   main, empty. Record the creation date in this prompt.
2. PyAutoMind/repos.yaml: add the row — category: organ, organ: Cortex,
   role prose "The Cortex — where the organism learns what is true: the science
   body map (projects.yaml) and the rulings of record for every science run;
   the science mirror of the Mind (runs and rulings, not prompts and PRs)".
   Run python3 scripts/repos_sync.py --write; commit the regenerated
   AGENTS.md routing table and every organ's map block it touches.
3. PyAutoBrain/ORGANISM.md: the organ row (:13-21) and the boundary prose,
   verbatim from the epic ledger: the Mind decides what to build, the Brain
   routes the work and executes nothing, the Cortex learns what is true. Add
   the sibling sentence beside Gut's ("the storage mirror of Memory"): the
   Cortex is the science mirror of the Mind. State the ruling-of-record rule in
   one sentence.
4. PyAutoBrain/docs/organs/cortex.md beside the six existing organ pages —
   short, same register, linking the epic ledger.
5. PyAutoBrain/board/_theme.py:70-110 ORGANS palette + :127 MARKS entry;
   config/policy.yaml:163-167 board family row (the board itself is phase 2 —
   the row only reserves the key); bin/install.sh:53,:70,:188 organ arrays
   (skills dir may be empty at birth — guard the symlink loop).
6. pyautolabs.github.io/index.html hub blurb so check_hub_blurb passes;
   PyAutoScientist/README.md is regenerated by step 2 — verify, do not hand-edit.
7. PyAutoBrain/AGENTS.md / CLAUDE.md: the one-line pointer the other organs
   have. Nothing else in Brain changes in this phase.

Acceptance

• The witness above, plus: pyauto-brain board renders without a KeyError on
  the new organ key; the Cortex repo contains only what step 1 created (the
  skeleton is phase 1 — do not pre-empt it here).
• PRs: PyAutoMind (body map + regenerated maps), PyAutoBrain (ORGANISM, docs,
  theme, policy, install), pyautolabs.github.io (blurb). PyAutoScientist only
  if repos_sync touched it.

Out of scope

• Any file in the Cortex repo beyond GitHub's own initial state (phase 1).
• The Brain conductor and Cortex dashboard (phase 2).
• A Cortex template / spawn.py rule (deferred, epic ledger).

[Jammy2211]

Shipped

Phase 0 of the cortex-birth epic: the Cortex is now an organ of record in the body map, and every generated organ surface follows the organ order Brain, Mind, Cortex, Memory, Heart, Hands, Nerves, Gut (ordinal prose dropped).

PRs, in merge order (Mind first — the sibling repos_sync --check legs compare against its body map):

1. repos.yaml: birth the Cortex organ row; organ order Brain, Mind, Cortex, Memory, Heart, Hands, Nerves, Gut (#377) #378 — repos.yaml Cortex organ row + organ block reorder; active.md / prompt updates (sha d8734225)
2. AGENTS.md: regenerate organism map for the Cortex organ (PyAutoMind#377) PyAutoGut#5 — regenerated organism map block (29907c15)
3. README: regenerate organ table for the Cortex (PyAutoMind#377) .github#8 — regenerated org-profile organ table (eeb0b45c)
4. README: regenerate organ table for the Cortex (PyAutoMind#377) PyAutoScientist#26 — regenerated README organ table (71024628)
5. index: name the Cortex in the organism blurb; organ order (PyAutoMind#377) pyautolabs.github.io#6 — hub blurb names the Cortex (e2fe7466)
6. ORGANISM: the Cortex, eighth organ — boundary prose, docs page, organ order (PyAutoMind#377) PyAutoBrain#328 — ORGANISM.md boundary prose + growth rule, docs/organs/cortex.md + toctree + RTD organism summary, README organ count, SIBLING_ORGANS, WITNESS_EXEMPT entry, regenerated map block, order-only edits to policy.yaml / _theme.py / install.sh (3ea67da7)
7. AGENTS.md: regenerate organism map for the Cortex organ (PyAutoMind#377) PyAutoNerves#158 — regenerated organism map block (026644df)

Witness: python3 PyAutoMind/scripts/repos_sync.py --check — 15 legs OK, exit 0. Tests: PyAutoBrain 691 passed (py3.12 + py3.13 in CI, docs build green); PyAutoMind 307 passed (lifecycle_drift, dashboard_refresh, spawn_drift privacy legs green); PyAutoNerves unittest 3.12 / 3.13 / nojax green. Gut, .github, PyAutoScientist and the hub have no PR checks configured; merged under the human's /prm.

Human step: PyAutoLabs/PyAutoCortex created 2026-09-01 (public, empty, not cloned locally in phase 0).

Deviations from the prompt (approved on this issue):

• No board/_theme.py ORGANS palette / MARKS entry and no config/policy.yaml boards row — deferred to phase 2 with the board and a logo (Gut and Nerves have none either; a boards: key without a palette fails test_board_theme).
• No bin/install.sh Cortex organ-array entry — deferred to phase 1 with the skeleton.
• Dashboard files dropped from the Mind PR: the boards footer renders from PyAutoBrain main's policy.yaml, which the Brain PR reorders; the close-out regenerates it from the merged Brain.

Ordering rule applied: organ blocks and tables in repos.yaml, ORGANISM.md, policy.yaml, _theme.py, install.sh, SIBLING_ORGANS, every regenerated map block and public table, and the hub blurb.

Phase 1 (draft/feature/pyautocortex/cortex_schema_and_skeleton.md) is unblocked.