[Jammy2211]

Phase 3 (last) of the cortex-checkin epic — #12. The Cortex half of PyAutoBrain#351.

Stacked on #350 / #11 — retargets to main as the stack merges. Base is feature/cortex-checkin-p2-the-door, itself based on feature/cortex-checkin-p1-shed-review-slot. Merge order for the epic's six PRs: PyAutoBrain#348 → #10 → PyAutoBrain#350 → #11 → PyAutoBrain#351 → this PR. Brain before Cortex within each phase: the Cortex dashboard_refresh.yml workflow renders through PyAutoBrain main, so the pages here go stale-red until the matching Brain PR has landed.

A rendered ## Where to look — and the check rule it now needs

PyAutoBrain#351 gives the dashboard a ## By project section and makes pyauto-brain cortex checkin print the same tree. Both render each phase's ## Where to look bullets verbatim, as the human's answer to which folder do I open. The section stops being a parser input and becomes a rendered promise — so check now holds it to one:

A phase whose State: is past planned must carry at least one ## Where to look bullet that is not the template placeholder (the output path, once there is one).

planned is exempt: there the placeholder is honest, and it is what new writes. Every phase in this tree already passes — the rule is a floor against future placeholder-only phases rendering a hole in the by-project view exactly where a human is being asked to act.

One consequence, fixed here: a legacy-born new (--legacy-run / --legacy-wrong, which requires --where and is born ready, not planned) used to write the placeholder even though it already knew where to look. It now writes the --where quarantine path as the bullet. The existing test_new_legacy_born_phase_is_ready_and_pullable caught this.

REFERENCE.md

• ## Where to look — a paragraph in the phase-anatomy section saying the bullets are rendered, where, and stating the new rule.
• The by-project view — what a project block holds, why it leads the board, and that the same tree is census --by-project, the check-in's closing summary and the dashboard section (one builder, three renderings).
• The five starting prompts — a state table: rule on it / accept and open phase N+1 / run it again / where the jobs stand / submit it, with the two new ones written out: how accept-and-open prefills from the tree (a planned or gated sibling numbered N+1 is opened, not duplicated; a taken number is named and the lowest free one offered), the new title-prefix rule (new writes # <Project> — phase N: in front of --title itself), and why run-it-again is a ruling first.
• The conductor CLI block — census --by-project.
• The check bullet — the new rule joins the list.

The regenerated pages

dashboard.md / dashboard.html regenerated from inside this worktree with the Brain worktree's _cortex.py on the same stacked branch, and committed here. dashboard --check is current. The new section renders three project blocks (euclid, inference_programme, subhalo_validation) plus a folded line for the eight dormant projects with nothing open.

Testing

tests/test_cortex.py: 95 passed (2 new).

• test_where_to_look_must_name_somewhere_past_planned — the placeholder is clean on the planned phase and drift on the awaiting-ruling one, per this suite's "prove each leg FAILS" contract.
• test_a_new_phase_ships_the_placeholder_and_no_other_bullet — what new writes is exactly the string the rule exempts, and the phase it writes passes check.

python3 scripts/cortex.py check → OK on the real tree. The Brain side's 13 new tests are in PyAutoBrain#351.

Heart

RED at ship time, not acknowledged by a human. Exact reasons from pyauto-heart readiness --json: red "release validation FAILED (stage integrate)"; yellow "PyAutoArray: open PR 11d old". Both are release-chain facts about other repos; PyAutoCortex is not in the release chain, and this branch is docs, one check rule and the regenerated board. PR opened, nothing merged.

🤖 Generated with Claude Code

https://claude.ai/code/session_013HsZA1ufn3msgPiDFxEXa6