cortex: checkin.yaml replaces epics.md; board regenerated projects-first

.github/workflows/cortex_check.yml

@@ -17,7 +17,7 @@ on:
       - "rulings/**"
       - "batches/**"
       - "projects.yaml"
-      - "epics.md"
+      - "checkin.yaml"
       - "dashboard.md"
       - "dashboard.html"
       - "scripts/**"
@@ -29,7 +29,7 @@ on:
       - "rulings/**"
       - "batches/**"
       - "projects.yaml"
-      - "epics.md"
+      - "checkin.yaml"
       - "dashboard.md"
       - "dashboard.html"
       - "scripts/**"

.github/workflows/dashboard_refresh.yml

@@ -3,8 +3,9 @@ name: Dashboard Refresh
 # Keeps the generated Cortex pages (`dashboard.md`, linked from the README, and
 # `dashboard.html`, the Pages index) in step with the registry they describe.
 # The pages are rendered by PyAutoBrain's cortex conductor from `phases/`,
-# `rulings/`, `batches/`, `projects.yaml` and `epics.md`, so any push that files
-# a phase, moves it, records a run or lands a ruling makes them stale.
+# `rulings/`, `batches/`, `projects.yaml` and `checkin.yaml`, so any push that
+# files a phase, moves it, records a run, lands a ruling or stamps a check-in
+# makes them stale.
 #
 # Same shape as the Mind's dashboard_refresh.yml, and for the same reason: on
 # pull requests a stale page is an error the author fixes on the branch; on
@@ -33,7 +34,7 @@ on:
       - "rulings/**"
       - "batches/**"
       - "projects.yaml"
-      - "epics.md"
+      - "checkin.yaml"
       - "dashboard.md"
       - "dashboard.html"
   pull_request:
@@ -42,7 +43,7 @@ on:
       - "rulings/**"
       - "batches/**"
       - "projects.yaml"
-      - "epics.md"
+      - "checkin.yaml"
       - "dashboard.md"
       - "dashboard.html"
   workflow_dispatch:

.github/workflows/ledger_merge.yml

@@ -15,7 +15,7 @@ name: Cortex Ledger Merge
 # pushed it ever comes back.
 #
 # WHAT IT WILL AND WILL NOT MERGE. Only a branch whose whole diff is *ledger*:
-# `phases/`, `rulings/`, `batches/`, `epics.md`. The line is drawn by
+# `phases/`, `rulings/`, `batches/`, `checkin.yaml`. The line is drawn by
 # scripts/ledger_merge.py — a script, so it is testable and a session can
 # predict the verdict — and it is DEFAULT DENY: anything under `scripts/`,
 # `tests/`, `.github/`, `policy/`, `docs/`, `projects.yaml`, the prose pages,

AGENTS.md

@@ -77,8 +77,11 @@ human's turn. Full rules in [rulings/AGENTS.md](rulings/AGENTS.md).
   human's verbatim reviews under `reviews/`, kept because 13 rulings cite them
   and append-only for the merge gate: never modified, only added. Nothing
   writes new ones (the review-slot apparatus was retired 2026-09-03).
-- **`epics.md`** — the Cortex half of every split epic; `- mind-half:` names
-  the Mind entry by slug.
+- **`checkin.yaml`** — one key, `refreshed: <UTC ISO 8601>`: when the science
+  state was last actually checked in, written by `pyauto-brain cortex checkin
+  --apply` and read back by the board. It means *last check-in*, never last
+  render, so a doc-only push cannot fake freshness; the HTML board reddens it
+  on the reader's own clock once it is more than an hour old.
 - **`scripts/cortex.py`** — the one lifecycle script (stdlib only):
   - `check` — every structural rule, hermetic; `cortex check: OK` or `DRIFT`
     with one `  - …` line per finding, exit 1.
@@ -97,7 +100,7 @@ human's turn. Full rules in [rulings/AGENTS.md](rulings/AGENTS.md).
   (see "Driving the Cortex" below). They are ledger for the merge gate.
 - **`scripts/ledger_merge.py`** — the default-deny classifier behind
   `.github/workflows/ledger_merge.yml`: a `claude/**` push whose whole diff is
-  ledger (`phases/`, `rulings/`, `batches/`, `epics.md`, the two generated
+  ledger (`phases/`, `rulings/`, `batches/`, `checkin.yaml`, the two generated
   dashboards) lands on `main` by itself; anything else waits for a human — and
   that "anything else" includes an `AGENTS.md` or `TEMPLATE.md` *inside* a
   ledger dir, which is doctrine, not an entry. `python3

REFERENCE.md

@@ -86,7 +86,7 @@ GitHub ref — whatever a human would open.
 | `Runs:` | comma-separated job **stems** | the index of the `## Runs` body; equal to the set of body stems |
 | `Ruling:` | ruling id | the chain head (see "Rulings") |
 | `Review-minutes:` | integer | a seed, not a measurement |
-| `Epic:` | slug | shared with the Mind — the join key across the two dashboards |
+| `Epic:` | slug | OPTIONAL join key to a **Mind** epic; the Cortex keeps no epics file of its own |
 | `Filed:` | `YYYY-MM-DD` | |
 | `Migrated-from:` | source path or ledger anchor | the Mind prompt, review file or project-ledger entry this phase was transcribed from (phase 4 of the birth epic) |
 
@@ -174,7 +174,7 @@ PyAutoCortex/
 ├── LICENSE  .gitignore
 │
 ├── projects.yaml            ← the science body map — CODE, not ledger (read with PyYAML)
-├── epics.md                 ← the Cortex half of each split epic (`- mind-half:`)
+├── checkin.yaml             ← `refreshed: <UTC ISO>` — the last check-in stamp; LEDGER
 ├── dashboard.md             ← GENERATED board — cortex conductor (`dashboard --apply`); LEDGER
 ├── dashboard.html           ← GENERATED board, the Pages index; LEDGER
 │
@@ -409,7 +409,7 @@ deny**:
 | Ledger — merged automatically | Code — always a human |
 |---|---|
 | `phases/**`, `rulings/**`, `batches/**` | `scripts/`, `tests/`, `.github/`, `policy/`, `docs/` |
-| `epics.md` | `projects.yaml`, `README.md`, `AGENTS.md`, `REFERENCE.md`, … |
+| `checkin.yaml` | `projects.yaml`, `README.md`, `AGENTS.md`, `REFERENCE.md`, … |
 | `dashboard.md`, `dashboard.html` (generated) | **`AGENTS.md` / `TEMPLATE.md` inside a ledger dir** |
 | | anything unclassified — a new root file, a new top-level folder |
 | | **any modification or deletion under `rulings/` or `batches/`** (append-only) |
@@ -518,6 +518,23 @@ phase (the six legs below), moves `running → pulled → awaiting-ruling`,
 re-renders `dashboard.md` + `dashboard.html`, and prints a summary keyed **by
 project** — the last thing on screen, so a chat sees it first.
 
+### `checkin.yaml` — the last-check-in stamp
+
+One key, one line, committed and pushed with the ledger:
+
+```yaml
+refreshed: 2026-09-04T14:03:00Z
+```
+
+It records the last **check-in**, not the last render: `checkin --apply` (and
+`collect --apply`) writes it from the same stamp it scored against, before the
+pages are rendered, so a doc-only push that re-renders the board cannot fake
+freshness. The board reads it back as "Last check-in"; the HTML twin computes
+the age on the *viewer's* clock and reddens it past sixty minutes, because a
+static page cannot know when it is being read. Absent, the board says "never
+checked in". The file is stable between renders, so `dashboard --check` needs
+no rule for it.
+
 ### The by-project view
 
 The summary is a tree, and it is the same tree in three places: the
@@ -667,7 +684,7 @@ for exactly that reason.
 
 | Workflow | Trigger | Writes |
 |---|---|---|
-| `cortex_check.yml` | push/PR on `phases/ rulings/ batches/ projects.yaml epics.md dashboard.* scripts/ tests/` | nothing (`cortex.py check` + pytest) |
+| `cortex_check.yml` | push/PR on `phases/ rulings/ batches/ projects.yaml checkin.yaml dashboard.* scripts/ tests/` | nothing (`cortex.py check` + pytest) |
 | `dashboard_refresh.yml` | push to main + PR on the ledger paths and the two pages, nightly **03:35 UTC**, dispatch | `dashboard.md`, `dashboard.html` on main (3-attempt fetch/reset/render/commit/push); a PR run errors instead of healing |
 | `pages_dashboard.yml` | push to `dashboard.html`, dispatch | nothing in git — publishes `dashboard.html` as the Pages index |
 | `ledger_merge.yml` | push to `claude/**`, dispatch | merges a ledger-only branch into main |

checkin.yaml

@@ -0,0 +1 @@
+refreshed: 2026-09-04T17:18Z