From 1d36c6ee9495f7a52536a5d6e54d2eba6db1ee5d Mon Sep 17 00:00:00 2001
From: Jammy2211 <JNightingale2211@gmail.com>
Date: Tue, 1 Sep 2026 20:54:17 -0400
Subject: [PATCH] =?UTF-8?q?cortex:=20seed=20projects.yaml=20=E2=80=94=20th?=
 =?UTF-8?q?e=20science=20body=20map;=20planned=20status,=20note=20field;?=
 =?UTF-8?q?=20decisions=2050=E2=80=9352=20(PyAutoMind#382)?=
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Content-Transfer-Encoding: 8bit

Phase 3 of the Cortex birth epic seeds the empty map with eleven real rows —
four active/planned science projects and seven dormant git repos — and extends
the phase-1 grammar by exactly what those rows needed.

- `scripts/cortex.py`: `PROJECT_STATUSES` gains `planned`; `note` becomes the
  one optional field (`PROJECT_OPTIONAL_FIELDS`), so the closed field set and
  the empty-value rule both still fire.
- `projects.yaml`: rows for `inference_programme`, `subhalo_validation`,
  `euclid` (`remote: none` by ruling), `euclid_dr1_prelim` (`planned`), plus
  the seven dormant repos; header states the boundary — science repos are not
  added to PyAutoMind/repos.yaml.
- `REFERENCE.md` subset and field table follow; `docs/schema_decisions.md`
  50 (the schema extension), 51 (the pull manifest v1 schema, amending 40),
  52 (the euclid ruling and the dormant-row rules).
- `dashboard.md` / `dashboard.html` re-rendered; the Projects table lists
  every row.

Verified: `cortex.py check` OK; `yaml.safe_load(projects.yaml) == parse` True;
`pytest tests -q` 130 passed.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SESCzU1FcwktEAdTZfmf3j
---
 REFERENCE.md             |  17 ++--
 dashboard.html           |  15 +++-
 dashboard.md             |  14 ++-
 docs/schema_decisions.md |  75 +++++++++++++++-
 projects.yaml            | 183 ++++++++++++++++++++++++++++++++++-----
 scripts/cortex.py        |  12 ++-
 tests/test_cortex.py     |  43 ++++++++-
 7 files changed, 324 insertions(+), 35 deletions(-)

diff --git a/REFERENCE.md b/REFERENCE.md
index f3a4652..2e89b64 100644
--- a/REFERENCE.md
+++ b/REFERENCE.md
@@ -399,6 +399,7 @@ Real YAML, parsed with the stdlib by a ~40-line line loop. The subset:
 <key>:                        # column 0, ^[a-z][a-z0-9_]*$
   <field>: <scalar>           # exactly two spaces; fixed field set, unknown field = error
   sync_verbs: [pull, push]    # flow list of bare words — the only list
+  note: "free text"           # the one optional field
 ```
 
 - Scalars are bare unless they contain `#`, `:` or edge spaces, then
@@ -406,11 +407,17 @@ Real YAML, parsed with the stdlib by a ~40-line line loop. The subset:
 - Comments on their own line or after ` #`. Blank lines anywhere.
 - No block lists, no nesting beyond the two levels, no anchors, no `---`, no
   quoted keys.
-- Fields (all required): `remote` (`owner/repo` | `none`), `local_path`
-  (absolute laptop path — the Cortex-only exception to the workspace-paths
-  rule), `ral_root`, `mirror` (path | `none`), `sync_cli`, `sync_verbs`,
-  `ledger`, `witness_file` (glob), `partition` (`gpu | ral | both`),
-  `status` (`active | dormant`).
+- Fields (required): `remote` (`owner/repo` | `none` — PyAutoLabs for active
+  projects; a personal remote is recorded as a fact with a `note:`),
+  `local_path` (absolute laptop path — the Cortex-only exception to the
+  workspace-paths rule), `ral_root`, `mirror` (path | `none`), `sync_cli`,
+  `sync_verbs`, `ledger`, `witness_file` (glob), `partition`
+  (`gpu | ral | both`), `status` (`active | dormant | planned`).
+- `note` (free text) is the **one optional field**: a row may omit it, an
+  empty `note:` is drift, and any other field is still an unknown-field
+  error. A note holding `:` or `#` is quoted like any other scalar.
+- Science repos are **not** added to `PyAutoMind/repos.yaml` — that map is the
+  workspace, this one is the science.
 - A file with no rows parses to an empty map (`{}`); PyYAML returns `None`
   for a comment-only document, so the `yaml.safe_load(text) == parse(text)`
   parity test runs on the fixture, which has a row.
diff --git a/dashboard.html b/dashboard.html
index 19b49be..7eef8f9 100644
--- a/dashboard.html
+++ b/dashboard.html
@@ -234,7 +234,20 @@
 <a id="epics"></a><h2>Epics <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoCortex/blob/main/epics.md">markdown version</a></h2><p class="muted">Long-running programmes whose science half lives here; each card links its development half in the Mind.</p>
 <p class="muted">(no epics yet)</p>
 <a id="projects"></a><h2>Projects <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects.yaml">markdown version</a></h2><p class="muted">The science body map — where each project lives, what syncs it and where its witness lands.</p>
-<p class="muted">(the science body map is empty)</p>
+<table class="map">
+<tr><th>Project</th><th>Status</th><th>Partition</th><th>Sync</th><th>Witness</th></tr>
+<tr><td><b>concr</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>cowls_diana</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>euclid</b></td><td>active</td><td>both</td><td><code>hpc/sync</code></td><td><code>catalogue/**/*.csv</code></td></tr>
+<tr><td><b>euclid_dr1_prelim</b></td><td>planned</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>ic50_workspace</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>inference_programme</b></td><td>active</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/searches/**/*.json</code></td></tr>
+<tr><td><b>pj011646</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>profiling</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>slope_hierarchy</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>subhalo_simulations</b></td><td>dormant</td><td>both</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+<tr><td><b>subhalo_validation</b></td><td>active</td><td>ral</td><td><code>hpc/sync</code></td><td><code>results/**/*.json</code></td></tr>
+</table>
 <ul class="boards"><li class="muted" style="padding:.3rem 0">Boards:</li><li><a data-organ="brain" href="https://pyautolabs.github.io/PyAutoBrain/">Brain</a></li><li><a data-organ="mind" href="https://pyautolabs.github.io/PyAutoMind/">Mind</a></li><li><a data-organ="memory" href="https://pyautolabs.github.io/PyAutoMemory/">Memory</a></li><li><a data-organ="heart" href="https://pyautolabs.github.io/PyAutoHeart/">Heart</a></li><li><a data-organ="hands" href="https://pyautolabs.github.io/PyAutoHands/">Hands</a></li><li><a data-organ="organism" href="https://pyautolabs.github.io/PyAutoScientist/">Scientist</a></li></ul>
 <script>async function copyCmd(b){
   const cmd=b.dataset.cmd;
diff --git a/dashboard.md b/dashboard.md
index 775a1e6..5a56f93 100644
--- a/dashboard.md
+++ b/dashboard.md
@@ -56,7 +56,19 @@ Every science phase the Cortex is holding, on one page: what is waiting on your
 
 [markdown version](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects.yaml) — The science body map — where each project lives, what syncs it and where its witness lands.
 
-- _(the science body map is empty)_
+| Project | Status | Partition | Sync | Ledger | Witness |
+|---|---|---|---|---|---|
+| concr | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| cowls_diana | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| euclid | active | both | `hpc/sync` | `CLAUDE.md` | `catalogue/**/*.csv` |
+| euclid_dr1_prelim | planned | both | `hpc/sync` | `wiki/project/state.md` | `results/**/*.json` |
+| ic50_workspace | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| inference_programme | active | both | `hpc/sync` | `results/notes/inference/PROGRAMME.md` | `results/searches/**/*.json` |
+| pj011646 | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| profiling | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| slope_hierarchy | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| subhalo_simulations | dormant | both | `hpc/sync` | `README.md` | `results/**/*.json` |
+| subhalo_validation | active | ral | `hpc/sync` | `wiki/project/state.md` | `results/**/*.json` |
 
 ---
 
diff --git a/docs/schema_decisions.md b/docs/schema_decisions.md
index 58971a8..a8e1ebe 100644
--- a/docs/schema_decisions.md
+++ b/docs/schema_decisions.md
@@ -165,9 +165,11 @@ Choices made in phase 2 — the conductor, the board and the workflows
     and `subhalo_validation` writes no structured version stamp — and scoring
     an unobservable leg as PASS would manufacture evidence while scoring it
     FAIL would cry wolf. SUSPECT says exactly what is true: nobody looked.
-40. **The pull manifest is `<mirror or local_path>/.cortex/pull.json`:
+40. **(amended by 51)** **The pull manifest is
+    `<mirror or local_path>/.cortex/pull.json`:
     `{"pulled_at": <ISO>, "runs": {"<jobid>": {"checkpoint_bytes": <int>,
-    "checkpoint_mtime": <ISO>}}}`, written by each project's own sync CLI
+    "checkpoint_mtime": <ISO>}}}` (decision 51 adds `schema` and
+    `checkpoints`), written by each project's own sync CLI
     (phase 3), read by `collect` when present.** Why: "when was this pulled,
     and did the checkpoint grow?" is knowable only at the moment of the pull;
     the puller is the only process that can record it. Until the CLIs write
@@ -235,3 +237,72 @@ Choices made in phase 2 — the conductor, the board and the workflows
     leaf in the path first) because `witness_file` is project-wide and phases
     share one tree. Also: `submitted → pulled` is not an edge, so a `submitted`
     member is scored but left with a note rather than moved.
+
+50. **`projects.yaml` gains `status: planned` and one optional field,
+    `note:`; every other field stays required and an unknown field stays an
+    error.** Why: phase 3 seeds the map with rows the phase-1 grammar could
+    not spell. `euclid_dr1_prelim` exists as a decision before it exists as a
+    directory — `planned` says "these are the paths it will have" without
+    lying that the project is `active`, and without the row being invented
+    twice later. And a third of the seeded rows are only intelligible with a
+    sentence attached: why `euclid` has no PyAutoLabs remote, that a dormant
+    row's `ral_root` is planned rather than observed, that a personal remote
+    is a recorded fact and not a target. That sentence had nowhere to live but
+    a comment, and a comment is not readable by the conductor. `note` is
+    optional because most rows do not need one, and the field set stays closed
+    (`PROJECT_FIELDS + PROJECT_OPTIONAL_FIELDS`) so a typo is still caught; an
+    empty `note:` is drift, exactly like an empty required field.
+
+51. **The pull manifest is v1 — `schema`, `checkpoints`, `runs` — and
+    `checkpoints` is the table that is always filled** (supersedes the shape
+    in decision 40, which stands as the record of why the manifest exists):
+    ```json
+    {"schema": 1,
+     "pulled_at": "<ISO UTC>",
+     "checkpoints": {"<run dir relative to the pull root>":
+                     {"bytes": <int>, "mtime": "<ISO>"}},
+     "runs": {"<jobid or jobid_task>":
+              {"checkpoint_bytes": <int>, "checkpoint_mtime": "<ISO>"}}}
+    ```
+    Why the second table: decision 40 assumed the puller knows which job id
+    produced which checkpoint, and one of the two projects cannot — the
+    profiling CLI pulls a results tree that carries no job id at all. The run
+    directory path *is* nameable on both sides, so `checkpoints` is keyed by
+    it (relative to the pull root, the same root `collect` resolves the run
+    directory under) and is always written; `runs` is written only where the
+    CLI can link a job id to a run directory (subhalo's `.out` names the
+    sample). `collect` therefore looks up `runs[ident]` → `runs[stem]` →
+    `checkpoints[<run dir rel>]`, and a manifest with no `schema` key is read
+    as the phase-2 shape so nothing that already exists breaks.
+    Gathered in **one** `ssh "$HPC_HOST" "find '<ral_root>/output' -name
+    checkpoint.hdf5 -printf '%s %T@ %p\n'"` over the existing ControlMaster
+    mux, immediately before the manifest is written — one round trip, and the
+    sizes are RAL's own, not the laptop's guess. The write is **dry-run
+    guarded** (`status` calls `pull --dry-run`, and a dry run must not
+    manufacture evidence that a pull happened), and `.cortex/` is gitignored
+    in every project: it is pull state, like `output/`.
+    Key shape, corrected by the first real pull: the checkpoint lives at
+    `<run dir>/files/search_internal/checkpoint.hdf5`, so the `checkpoints` key is the
+    run directory — the grandparent of the file — with any trailing `/files` stripped.
+
+52. **`Science/euclid` gets `remote: none` by ruling, and the dormant rows
+    follow three rules.** The euclid ruling (2026-09-01): it tracks a
+    DR1-derived catalogue keyed by tile/RA/DEC
+    (`catalogue/inspection/failure_mode_breakdown_consensus75.csv`), it
+    already pushes to the personal remote `Jammy2211/euclid-dr1-modeling`, it
+    nests the Overleaf paper repo, and it is 34 GB with an `output/` too large
+    to `du`. Any one of those refuses a PyAutoLabs remote under the
+    no-Euclid-data rule; together they settle it. Nothing is lost, because the
+    project's code half is already at
+    `PyAutoLabs/euclid_strong_lens_modeling_pipeline` at parity — what stays
+    outside the org is data and prose. The row is still written, because the
+    Cortex must be able to name a project it will never host.
+    The dormant rules: **(a) git repos only** — `subhalo`, `euclid_group` and
+    the `z_*` trees are storage, and storage is not a project with a
+    lifecycle; **(b) an assistant clone is not a project** — `aris_PJ011646`
+    is a copy of a workspace, so `pj011646` is the row and the clone is not;
+    **(c) a personal remote is recorded as a fact, never as a target** —
+    `slope_hierarchy`, `pj011646`, `concr` and `ic50_workspace` push to
+    `Jammy2211/…` and the row says so in `remote:` with the reason in
+    `note:`, so nobody re-derives the answer to "should this move into the
+    org?" once a quarter.
diff --git a/projects.yaml b/projects.yaml
index 103e120..9dcd0a2 100644
--- a/projects.yaml
+++ b/projects.yaml
@@ -5,12 +5,17 @@
 # here is always a human's turn (scripts/ledger_merge.py leaves it for review,
 # exactly like PyAutoMind/repos.yaml).
 #
+# THE BOUNDARY. Science repos are NOT added to PyAutoMind/repos.yaml — that map
+# is the workspace; this one is the science. A project reaches the organism
+# through its row here and nowhere else.
+#
 # Schema — a restricted YAML subset that scripts/cortex.py parses with the
 # stdlib (REFERENCE.md "The restricted YAML subset"). It is also real YAML:
 # `yaml.safe_load` reads it identically, and a test keeps the two in step.
 #
 #   <key>:                        # column 0, ^[a-z][a-z0-9_]*$ — the project key
-#     remote: <owner/repo | none> # the private PyAutoLabs remote (code, config, wiki, witness files only)
+#     remote: <owner/repo | none> # the remote — PyAutoLabs for active projects; a
+#                                 # personal remote is recorded as a fact with a `note:`
 #     local_path: <abs path>      # the laptop checkout
 #     ral_root: <abs path>        # the project root on RAL (/mnt/ral/jnightin/<project>)
 #     mirror: <abs path | none>   # the laptop pull root the sync CLI fills (holds data, not science)
@@ -19,31 +24,169 @@
 #     ledger: <path>              # the project's own commentary ledger, relative to local_path
 #     witness_file: <glob>        # where a run's witness lands, relative to the mirror
 #     partition: gpu | ral | both # which SLURM partition(s) the project runs on
-#     status: active | dormant
+#     status: active | dormant | planned
+#     note: <text>                # OPTIONAL, and the only optional field — free text
+#                                 # about the row; an empty `note:` is drift
 #
 # Scalars are bare unless they contain `#`, `:` or edge spaces (then "..."
 # with no escapes); comments on their own line or after ` #`; no block lists,
-# no deeper nesting, no anchors, no `---`. Every field is required; an
-# unknown field is an error.
+# no deeper nesting, no anchors, no `---`. Every field but `note` is required;
+# an unknown field is an error.
 #
 # THE WORKSPACE-PATHS EXCEPTION. `local_path` and `mirror` are absolute laptop
 # paths OUTSIDE the PyAutoLabs workspace — the Science folder under /mnt/c/…
 # where the datasets, output trees and pulled results live. This file is the
 # one place in the organism that carries such a path; a phase file or a ruling
 # reaches a project through its row here, never with a bare path of its own.
-#
-# Worked example — the JAX inference programme, the project the schema was
-# stress-tested against. Real rows are seeded in phase 3 of the birth epic;
-# until then the map is empty.
-#
-# autolens_profiling:
-#   remote: PyAutoLabs/autolens_profiling
-#   local_path: /home/jammy/Code/PyAutoLabs/autolens_profiling
-#   ral_root: /mnt/ral/jnightin/autolens_profiling
-#   mirror: /mnt/c/Users/Jammy/Science/inference_programme
-#   sync_cli: hpc/sync
-#   sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
-#   ledger: results/notes/inference/PROGRAMME.md
-#   witness_file: results/searches/**/*.json
-#   partition: both
-#   status: active
+
+# --------------------------------------------------------------------------- #
+# active
+# --------------------------------------------------------------------------- #
+inference_programme:
+  remote: PyAutoLabs/autolens_profiling
+  local_path: /home/jammy/Code/PyAutoLabs/autolens_profiling
+  ral_root: /mnt/ral/jnightin/autolens_profiling
+  mirror: /mnt/c/Users/Jammy/Science/inference_programme
+  sync_cli: hpc/sync
+  sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
+  ledger: results/notes/inference/PROGRAMME.md
+  witness_file: results/searches/**/*.json
+  partition: both
+  status: active
+  note: "DECISIONS.md is commentary; pull-only CLI — RAL is a git checkout; gpu-1 excluded"
+
+subhalo_validation:
+  remote: PyAutoLabs/subhalo_validation
+  local_path: /mnt/c/Users/Jammy/Science/subhalo_validation
+  ral_root: /mnt/ral/jnightin/subhalo_validation
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
+  ledger: wiki/project/state.md
+  witness_file: results/**/*.json
+  partition: ral
+  status: active
+  note: "pulls land in the checkout (PULL_DIRS output results); run_chain.sh chains A→B afterok; witness evidence_increase < 5, subhalo_stage, test_mode"
+
+euclid:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/euclid
+  ral_root: /mnt/ral/jnightin/euclid_strong_lens_modeling_pipeline
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [push, pull, sync, status]
+  ledger: CLAUDE.md
+  witness_file: catalogue/**/*.csv
+  partition: both
+  status: active
+  note: "NO PyAutoLabs remote by ruling 2026-09-01: tracks DR1 tile-keyed catalogue CSV, personal remote Jammy2211/euclid-dr1-modeling, nested Overleaf paper repo, 34 GB; code half = PyAutoLabs/euclid_strong_lens_modeling_pipeline; witness undefined until a science phase pre-registers one"
+
+euclid_dr1_prelim:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/euclid_dr1_prelim
+  ral_root: /mnt/ral/jnightin/euclid_dr1_prelim
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [push, pull, sync, status]
+  ledger: wiki/project/state.md
+  witness_file: results/**/*.json
+  partition: both
+  status: planned
+  note: "created by euclid-dr1-prep phase 4 (a Cortex phase after migration); every path is the planned one"
+
+# --------------------------------------------------------------------------- #
+# dormant — git repos only. The non-git trees (subhalo, euclid_group, z_*) are
+# storage, not projects, and aris_PJ011646 is an assistant clone; none get a
+# row. `ral_root` is the planned path and `sync_verbs` is unverified on every
+# row below — each note says so.
+# --------------------------------------------------------------------------- #
+profiling:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/profiling
+  ral_root: /mnt/ral/jnightin/profiling
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "2026-05 checkpointed sweep harness, PyAutoNSS venv; name collides with autolens_profiling; ral_root planned, sync_verbs unverified"
+
+cowls_diana:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/cowls_diana
+  ral_root: /mnt/ral/jnightin/cowls_diana
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "local git, no remote; ral_root planned, sync_verbs unverified"
+
+subhalo_simulations:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/subhalo_simulations
+  ral_root: /mnt/ral/jnightin/subhalo_simulations
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "git init, zero commits, 21 GB; ral_root planned, sync_verbs unverified"
+
+slope_hierarchy:
+  remote: Jammy2211/slope_hierarchy
+  local_path: /mnt/c/Users/Jammy/Science/slope_hierarchy
+  ral_root: /mnt/ral/jnightin/slope_hierarchy
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "personal remote, recorded as a fact — not a PyAutoLabs repo; ral_root planned, sync_verbs unverified"
+
+pj011646:
+  remote: Jammy2211/PJ011646
+  local_path: /mnt/c/Users/Jammy/Science/PJ011646
+  ral_root: /mnt/ral/jnightin/PJ011646
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "personal remote, recorded as a fact — not a PyAutoLabs repo; ral_root planned, sync_verbs unverified"
+
+concr:
+  remote: Jammy2211/cosmology_and_cancer
+  local_path: /mnt/c/Users/Jammy/Science/concr
+  ral_root: /mnt/ral/jnightin/concr
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "personal remote Jammy2211/cosmology_and_cancer, recorded as a fact; ral_root planned, sync_verbs unverified"
+
+ic50_workspace:
+  remote: Jammy2211/ic50_workspace
+  local_path: /mnt/c/Users/Jammy/Science/ic50_workspace
+  ral_root: /mnt/ral/jnightin/ic50_workspace
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  witness_file: results/**/*.json
+  partition: both
+  status: dormant
+  note: "personal remote, recorded as a fact — not a PyAutoLabs repo; ral_root planned, sync_verbs unverified"
diff --git a/scripts/cortex.py b/scripts/cortex.py
index 9b4b302..c215e48 100644
--- a/scripts/cortex.py
+++ b/scripts/cortex.py
@@ -94,8 +94,12 @@
 
 PROJECT_FIELDS = ("remote", "local_path", "ral_root", "mirror", "sync_cli",
                   "sync_verbs", "ledger", "witness_file", "partition", "status")
+#: the one optional field — free text about the row (why a remote is `none`,
+#: what a verb does). A row may omit it; an empty `note:` is still drift, and
+#: any field outside these two tuples is still an error.
+PROJECT_OPTIONAL_FIELDS = ("note",)
 PARTITIONS = ("gpu", "ral", "both")
-PROJECT_STATUSES = ("active", "dormant")
+PROJECT_STATUSES = ("active", "dormant", "planned")
 
 # --------------------------------------------------------------------------- #
 # grammars (REFERENCE.md)
@@ -335,7 +339,7 @@ def parse_projects(text: str) -> "tuple[dict[str, dict], list[str]]":
         m = PROJECT_FIELD_RE.match(line)
         if m and current is not None:
             field, value = m.group(1), (m.group(2) or "")
-            if field not in PROJECT_FIELDS:
+            if field not in PROJECT_FIELDS + PROJECT_OPTIONAL_FIELDS:
                 problems.append(f"{where}: unknown field `{field}` on {current}")
                 continue
             if field in rows[current]:
@@ -374,8 +378,8 @@ def _finish_row(key: str, row: dict, problems: "list[str]") -> None:
         problems.append(f"projects.yaml: {key}.partition must be gpu | ral | both, "
                         f"not {row['partition']}")
     if row.get("status") and row["status"] not in PROJECT_STATUSES:
-        problems.append(f"projects.yaml: {key}.status must be active | dormant, "
-                        f"not {row['status']}")
+        problems.append(f"projects.yaml: {key}.status must be "
+                        f"active | dormant | planned, not {row['status']}")
     remote = row.get("remote")
     if remote and remote != "none" and not re.match(r"^[\w.-]+/[\w.-]+$", remote):
         problems.append(f"projects.yaml: {key}.remote must be owner/repo or none")
diff --git a/tests/test_cortex.py b/tests/test_cortex.py
index e565107..d6aa08b 100644
--- a/tests/test_cortex.py
+++ b/tests/test_cortex.py
@@ -184,12 +184,25 @@ def test_gate_ref_regex_rejects_owner_repo_form():
 # projects.yaml — the restricted subset
 # --------------------------------------------------------------------------- #
 def test_comment_only_projects_yaml_parses_to_an_empty_map():
-    rows, problems = cortex.parse_projects((REPO / "projects.yaml").read_text())
-    assert rows == {} and problems == []
     rows, problems = cortex.parse_projects((EMPTY / "projects.yaml").read_text())
     assert rows == {} and problems == []
 
 
+def test_the_live_body_map_parses_clean_and_matches_pyyaml():
+    """The seeded map (phase 3) is the real witness for the subset: it is the
+    only file that exercises `planned`, `note`, and a 17-verb flow list."""
+    yaml = pytest.importorskip("yaml")
+    text = (REPO / "projects.yaml").read_text()
+    rows, problems = cortex.parse_projects(text)
+    assert problems == []
+    assert yaml.safe_load(text) == rows
+    assert {"inference_programme", "subhalo_validation", "euclid",
+            "euclid_dr1_prelim"} <= set(rows)
+    assert rows["euclid_dr1_prelim"]["status"] == "planned"
+    assert rows["euclid"]["remote"] == "none"
+    assert "PyAutoLabs remote" in rows["euclid"]["note"]
+
+
 def test_projects_parse_matches_pyyaml_on_the_fixture():
     yaml = pytest.importorskip("yaml")
     text = (SKELETON / "projects.yaml").read_text()
@@ -224,6 +237,32 @@ def test_missing_projects_field_and_bad_enums(tmp_path):
     _assert_drift(root, "example is missing ledger", "partition must be gpu | ral | both")
 
 
+def test_planned_is_a_legal_status(tmp_path):
+    root = _copy(tmp_path)
+    _edit(root, "projects.yaml", "  status: active\n", "  status: planned\n")
+    assert _problems(root) == []
+    _edit(root, "projects.yaml", "  status: planned\n", "  status: someday\n")
+    _assert_drift(root, "status must be active | dormant | planned")
+
+
+def test_note_is_optional_but_never_empty_and_the_field_set_still_closes(tmp_path):
+    """`note` is the one field a row may omit. An empty one is still drift,
+    and everything outside the field set is still an unknown field."""
+    root = _copy(tmp_path)
+    assert _problems(root) == [], "the fixture carries no `note:`"
+    _edit(root, "projects.yaml", "  status: active\n",
+          '  status: active\n  note: "a fact: with a colon # and a hash"\n')
+    assert _problems(root) == []
+    rows, problems = cortex.parse_projects((root / "projects.yaml").read_text())
+    assert problems == [] and rows["example"]["note"] == \
+        "a fact: with a colon # and a hash"
+    yaml = pytest.importorskip("yaml")
+    assert yaml.safe_load((root / "projects.yaml").read_text()) == rows
+    _edit(root, "projects.yaml", '  note: "a fact: with a colon # and a hash"\n',
+          "  note:\n")
+    _assert_drift(root, "example.note is empty")
+
+
 def test_projects_outside_the_subset(tmp_path):
     root = _copy(tmp_path)
     _edit(root, "projects.yaml", "  sync_verbs: [pull, submit, jobs, tail]\n",