Affected Repositories

• PyAutoBrain (primary — conductor verb, skill, tests)
• PyAutoCortex (scripts/cortex.py birth, tests, docs)

Branch Survey

Suggested branch: feature/cortex-birth

Implementation Steps

1. PyAutoCortex/scripts/cortex.py: birth_project(root, key, row: dict, summary, today, issue, now) validates the key regex, that the key is unused, that local_path is unused, and that the fields are complete and quotable. It appends the row block at the end of projects.yaml in PROJECT_FIELDS order, re-reads it with load_projects (restoring the file on any problem), then new_ledger. CLI birth <key> --local-path … --ral-root … --remote … --sync-verbs a,b --ledger … --assistant … --partition … --witness-file … --summary … [--issue] [--note]. Tests in tests/.
2. PyAutoBrain/agents/conductors/cortex/_cortex.py: birth_row(projects, key, category, assistant, …) derives the fields. The Science root comes from science_root_from. The RAL base is the most common <base> of the category-shaped ral_roots. Remote from git remote get-url origin → owner/repo. sync_verbs from the hpc/sync case labels. Ledger wiki/project/state.md → README.md fallback. cmd_birth dry-run prints the row. --apply: push_preflight, cut claude/birth-<key>, subprocess cortex.py birth, commit, ledger_merge.py classify --base origin/main (push only on 0), back to main, then drift_report filtered to the key.
3. skills/cortex (Brain): a "Starting a new project" section.
4. Docs: Cortex REFERENCE.md, AGENTS.md, docs/schema_decisions.md 63; conductor AGENTS.md.
5. Tests: Brain conductor (derivation, dry-run writes nothing, refusals: no folder, existing key or path, wrong category) and Cortex (birth appends, rolls back, refuses duplicates).
6. Verify end-to-end on a throwaway Cortex clone, never the real main: scaffold a dummy project dir, birth --apply --no-push, then drift is clean for it.

Key Files

• PyAutoCortex/scripts/cortex.py, PyAutoCortex/tests/
• PyAutoBrain/agents/conductors/cortex/_cortex.py, PyAutoBrain/tests/test_cortex_conductor.py, PyAutoBrain/skills/cortex/

Cortex birth: scaffold, seed and register a Science project in one step

Type: feature
Target: cortex
Repos:

• PyAutoBrain
• PyAutoCortex
  Themes:
• science
• cortex
  Difficulty: medium
  Autonomy: human-required
  Priority: high
  Status: formalised
  Consequence: judge
  Filed: 2026-10-29
  Parent: complete/2026/10/cortex-science-drift.md

Original request (verbatim)

"5) Bring this all together with PyAutoCortex which needs to become the main tool to manage Science
projects, its meant to be but hasnt been used as such for a while."

Follow-up (2026-10-29), approving the proposed next steps including "a new-project command that
scaffolds a project in active/ or development/, seeds it from dataset/ or simulators/ and
registers it in one step": "yeah do it", then "Merge, then Phase 2".

Context

Phase 1 (cortex drift, PyAutoBrain#544) shipped 2026-10-29: the register and the Science tree are
now compared on every census/check-in. Today a new project is started by hand-copying an older one,
so it gets no row and the drift check reports it as unregistered. Science layout:
/mnt/c/Users/Jammy/Workspace/Science/{active,development,complete,archive,dataset,simulators};
simulators share --dataset-path / --dataset-types (Science/simulators/AGENTS.md).

Scope (revised 2026-10-29, human-approved: "yes, file it and go")

Scaffolding stays with the domain assistant: autolens_assistant / autofit_assistant
skills/start-new-project.md is the single science-project skill, and the public assistants must
not learn the private Science tree or the Cortex. The Cortex adds only the registration half:

• pyauto-brain cortex birth <key> --category active|development --assistant <name> --summary "<one line>" [--issue Repo#N] [--apply]: checks Science/<category>/<key>/
  exists and has no row; derives local_path, ral_root (<ral base>/<category>/<key>, base
  from the other rows), sync_cli / sync_verbs from the scaffolded hpc/sync, partition,
  witness_file and remote (git origin or none); writes the row and runs cortex.py new
  on a claude/birth-<key> branch (an add-only birth diff, which lands by itself); then runs
  drift for the new project. Dry run by default. Never creates a GitHub remote or touches RAL;
  it prints those lines for the human.
• The Brain's cortex skill gains a "new project" section: run the assistant's
  start-new-project with the target Science/<category>/<key>, seed dataset/ from
  Science/dataset/<sample> or Science/simulators/<type>/<lens>.py --dataset-path dataset,
  then cortex birth.
• Docs: Cortex REFERENCE.md (birth) and schema decision 63.

Out of scope

Moving trees on RAL; output summaries on the board (draft/feature/cortex/output_summary.md).