refactor: repoint RAL paths to the category layout, phase 2

dashboard.md

@@ -12,7 +12,7 @@ One ledger per science project: what is on the cluster right now, what the human
 |-------|------:|
 | [Running](#projects) | 22 |
 | [Open](#projects) | 47 |
-| [Projects](#projects) | 8 |
+| [Projects](#projects) | 9 |
 
 <details><summary>📋 check in since last time</summary>
 
@@ -43,6 +43,7 @@ Last check-in: 2026-09-30T09:51Z.
 | Project | Running | Open | Last update |
 |---|---:|---:|---|
 | subhalo_validation | 0 | 5 | 2026-09-07 |
+| subhalo | 0 | 0 | 2026-10-15 |
 | euclid_dr1 | 16 | 42 | 2026-10-10 |
 | analytic_gaussian | 0 | 0 | 2026-10-14 |
 | ep_toy_gaussian | 0 | 0 | 2026-10-14 |
@@ -55,7 +56,7 @@ Last check-in: 2026-09-30T09:51Z.
 
 ### subhalo_validation — Do the SLaM subhalo pipelines false-detect on lenses with no subhalo
 
-active · ral · [subhalo_validation#2](https://github.com/PyAutoLabs/subhalo_validation/issues/2) · [projects/subhalo_validation.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/subhalo_validation.md) · local `/mnt/c/Users/Jammy/Science/active/subhalo_validation` · RAL `/mnt/ral/jnightin/subhalo_validation`
+active · ral · [subhalo_validation#2](https://github.com/PyAutoLabs/subhalo_validation/issues/2) · [projects/subhalo_validation.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/subhalo_validation.md) · local `/mnt/c/Users/Jammy/Science/active/subhalo_validation` · RAL `/mnt/ral/jnightin/active/subhalo_validation`
 
 **Now**
 
@@ -88,6 +89,32 @@ Use the cortex skill. — resume subhalo_validation: read PyAutoCortex projects/
 
 </details>
 
+### subhalo — SLaM subhalo modelling of the SLACS lens sample
+
+active · both · no issue yet · [projects/subhalo.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/subhalo.md) · local `/mnt/c/Users/Jammy/Science/active/subhalo` · RAL `/mnt/ral/jnightin/active/subhalo`
+
+**Now**
+
+Registered 2026-10-15 (PyAutoCortex#67): SLACS sample under dataset/, output/ empty, no runs yet; ral_root not yet created on RAL — the first hpc/sync push creates it.
+
+**Runs**
+
+- _nothing on the cluster_
+
+**Last 5**
+
+- 2026-10-15 — *note* — ledger opened
+
+[full log](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/subhalo.md)
+
+<details><summary>📋 resume subhalo</summary>
+
+```
+Use the cortex skill. — resume subhalo: read PyAutoCortex projects/subhalo.md (Now, Runs, Log) and then /mnt/c/Users/Jammy/Science/active/subhalo/README.md and the assistant autolens_assistant's AGENTS.md; tell me where I left off and what I said I would do next. Submit nothing and log nothing until I say.
+```
+
+</details>
+
 ### euclid_dr1 — Does the sep1 DR1 delivery reproduce the ten prelim lenses by eye
 
 active · ral · no issue yet · [projects/euclid_dr1.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/euclid_dr1.md) · local `/mnt/c/Users/Jammy/Science/euclid_dr1` · RAL `/mnt/ral/jnightin/euclid_dr1`
@@ -237,7 +264,7 @@ Use the cortex skill. — resume ep_toy_gaussian: read PyAutoCortex projects/ep_
 
 ### slope_hierarchy_scale — Hierarchical slope recovery with graphical and EP at N=25 to 50
 
-active · both · [slope_hierarchy_scale#2](https://github.com/PyAutoLabs/slope_hierarchy_scale/issues/2) · [projects/slope_hierarchy_scale.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/slope_hierarchy_scale.md) · local `/mnt/c/Users/Jammy/Science/active/slope_hierarchy_scale` · RAL `/mnt/ral/jnightin/slope_hierarchy_scale`
+active · both · [slope_hierarchy_scale#2](https://github.com/PyAutoLabs/slope_hierarchy_scale/issues/2) · [projects/slope_hierarchy_scale.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/slope_hierarchy_scale.md) · local `/mnt/c/Users/Jammy/Science/active/slope_hierarchy_scale` · RAL `/mnt/ral/jnightin/active/slope_hierarchy_scale`
 
 **Now**
 
@@ -267,7 +294,7 @@ Use the cortex skill. — resume slope_hierarchy_scale: read PyAutoCortex projec
 
 ### ic50_workspace — EP against the graphical joint fit on IC50 dose-response data, scaling up
 
-active · ral · [PyAutoCortex#36](https://github.com/PyAutoLabs/PyAutoCortex/issues/36) · [projects/ic50_workspace.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/ic50_workspace.md) · local `/mnt/c/Users/Jammy/Science/active/ic50_workspace` · RAL `/mnt/ral/jnightin/ic50_workspace`
+active · ral · [PyAutoCortex#36](https://github.com/PyAutoLabs/PyAutoCortex/issues/36) · [projects/ic50_workspace.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/ic50_workspace.md) · local `/mnt/c/Users/Jammy/Science/active/ic50_workspace` · RAL `/mnt/ral/jnightin/active/ic50_workspace`
 
 **Now**
 
@@ -297,7 +324,7 @@ Use the cortex skill. — resume ic50_workspace: read PyAutoCortex projects/ic50
 
 ### autolens_inference — Do the PyAutoLens inference backends agree on the HST SLaM posterior
 
-active · both · [autolens_inference#4](https://github.com/PyAutoLabs/autolens_inference/issues/4) · [projects/autolens_inference.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/autolens_inference.md) · local `/home/jammy/Code/PyAutoLabs/lens/autolens_inference` · RAL `/mnt/ral/jnightin/autolens_inference`
+active · both · [autolens_inference#4](https://github.com/PyAutoLabs/autolens_inference/issues/4) · [projects/autolens_inference.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/autolens_inference.md) · local `/home/jammy/Code/PyAutoLabs/lens/autolens_inference` · RAL `/mnt/ral/jnightin/inference/autolens_inference`
 
 **Now**
 
@@ -332,7 +359,7 @@ Use the cortex skill. — resume autolens_inference: read PyAutoCortex projects/
 
 ### autofit_inference — PyAutoFit search benchmark on gaussian_x3: which searches find the right answer fastest
 
-active · ral · [autofit_inference#8](https://github.com/PyAutoLabs/autofit_inference/issues/8) · [projects/autofit_inference.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/autofit_inference.md) · local `/home/jammy/Code/PyAutoLabs/fit/autofit_inference` · RAL `/mnt/ral/jnightin/autofit_inference`
+active · ral · [autofit_inference#8](https://github.com/PyAutoLabs/autofit_inference/issues/8) · [projects/autofit_inference.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/autofit_inference.md) · local `/home/jammy/Code/PyAutoLabs/fit/autofit_inference` · RAL `/mnt/ral/jnightin/inference/autofit_inference`
 
 **Now**
 
@@ -360,20 +387,21 @@ Use the cortex skill. — resume autofit_inference: read PyAutoCortex projects/a
 
 </details>
 
-### euclid — The original Euclid DR1 grade-AB catalogue project, superseded by euclid_dr1_prelim
+### euclid — The original Euclid DR1 grade-AB catalogue project, superseded by euclid_dr1
 
-dormant · both · no issue yet · [projects/euclid.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/euclid.md) · local `/mnt/c/Users/Jammy/Science/active/euclid` · RAL `/mnt/ral/jnightin/euclid_strong_lens_modeling_pipeline`
+dormant · both · no issue yet · [projects/euclid.md](https://github.com/PyAutoLabs/PyAutoCortex/blob/main/projects/euclid.md) · local `/mnt/c/Users/Jammy/Science/active/euclid` · RAL `/mnt/ral/jnightin/active/euclid`
 
 **Now**
 
-Dormant since 2026-09-07: superseded by euclid_dr1_prelim. Three questions were planned and never run (see the archive).
+Dormant: superseded by euclid_dr1 (euclid_dr1_prelim is defunct). The tree is kept under Science/active and RAL `active/euclid` (category layout, 2026-10-15); no question is open.
 
 **Runs**
 
 - _nothing on the cluster_
 
 **Last 5**
 
+- 2026-10-15 — *note* — superseded by euclid_dr1 (euclid_dr1_prelim defunct) per the human; stays dormant; folder under Science/active and RAL active/; ral_root repointed to the category layout (PyAutoCortex#67)
 - 2026-08-28 — *note* — question: Do we recover Sersic indices or is prior pile-up artefact — planned, never run [archive/tasks/euclid/sersic_index_recovery.md]
 - 2026-08-28 — *note* — question: Can a fitted Euclid lens be resimulated and recovered — planned, never run [archive/tasks/euclid/resimulate_fitted_lens_simulator.md]
 - 2026-08-28 — *note* — question: How robust are magnification estimates under model match and mismatch — planned, never run [archive/tasks/euclid/magnification_robustness.md]

docs/schema_decisions.md

@@ -463,3 +463,15 @@ Choices made in phase 2 — the conductor, the board and the workflows
     ask; the agent records only cluster facts), and the top of each project's
     GitHub issue is the same concise ledger the board shows (the `issue`
     block), with the detailed run-through underneath it.
+
+61. **`ral_root` follows the category layout, and `subhalo` gets a row**
+    (2026-10-15, PyAutoCortex#67). On 2026-10-15 the human moved the RAL
+    project trees under `/mnt/ral/jnightin/` into category folders mirroring
+    the laptop Science tree: `active/`, `archive/`, `complete/`, plus
+    `inference/` and `profiling/` for the repo-backed campaign roots;
+    `PyAuto/`, `euclid_dr1/` and `scratch/` stay top-level. Every row's
+    `ral_root` now mirrors its `local_path` category (a top-level laptop tree
+    keeps a top-level `ral_root`). The non-git `Science/active/subhalo` tree
+    is registered `active` by human decision, the one exception to 52(a): an
+    active project needs a ledger, and git is not what makes it science.
+    Why: one layout on both machines means a path is derived, never looked up.

projects.yaml

@@ -17,7 +17,7 @@
 #     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>)
+#     ral_root: <abs path>        # the project root on RAL (/mnt/ral/jnightin/<category>/<project>)
 #     mirror: <abs path | none>   # the laptop pull root the sync CLI fills (holds data, not science)
 #     sync_cli: <path>            # the project's sync CLI, relative to local_path
 #     sync_verbs: [a, b, c]       # the verbs that CLI has — a flow list of bare words, the only list
@@ -48,7 +48,7 @@
 inference_programme:
   remote: PyAutoLabs/autolens_profiling
   local_path: /home/jammy/Code/PyAutoLabs/lens/autolens_profiling
-  ral_root: /mnt/ral/jnightin/autolens_profiling
+  ral_root: /mnt/ral/jnightin/profiling/autolens_profiling
   mirror: /mnt/c/Users/Jammy/Science/archive/inference_programme
   sync_cli: hpc/sync
   sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
@@ -62,7 +62,7 @@ inference_programme:
 subhalo_validation:
   remote: PyAutoLabs/subhalo_validation
   local_path: /mnt/c/Users/Jammy/Science/active/subhalo_validation
-  ral_root: /mnt/ral/jnightin/subhalo_validation
+  ral_root: /mnt/ral/jnightin/active/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]
@@ -73,10 +73,24 @@ subhalo_validation:
   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"
 
+subhalo:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Science/active/subhalo
+  ral_root: /mnt/ral/jnightin/active/subhalo
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [push, pull, sync, status]
+  ledger: README.md
+  assistant: autolens_assistant
+  witness_file: results/**/*.json
+  partition: both
+  status: active
+  note: "registered 2026-10-15 by human decision (PyAutoCortex#67), overriding schema decision 52(a) for this tree: not a git repo, so remote none; ledger is the generic PyAutoLens project-template README; SLACS sample under dataset/, output/ empty, no results/ yet; hpc/sync.conf targets HPC_BASE=/mnt/ral/jnightin/active; batch_cpu submits still say --partition=cpu (no such partition on RAL); ral_root not yet created on RAL; witness undefined until a science task pre-registers one"
+
 euclid:
   remote: none
   local_path: /mnt/c/Users/Jammy/Science/active/euclid
-  ral_root: /mnt/ral/jnightin/euclid_strong_lens_modeling_pipeline
+  ral_root: /mnt/ral/jnightin/active/euclid
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, sync, status]
@@ -85,12 +99,12 @@ euclid:
   witness_file: catalogue/**/*.csv
   partition: both
   status: dormant
-  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 task pre-registers one; dormant 2026-09-07: superseded by euclid_dr1_prelim, which phase 4 births; local output/ cleared 2026-09-07 (60 GB of May–June DR1 grade_ab runs, still on RAL under /mnt/ral/jnightin/euclid)"
+  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 task pre-registers one; dormant 2026-09-07: superseded by euclid_dr1_prelim, which phase 4 births; local output/ cleared 2026-09-07 (60 GB of May–June DR1 grade_ab runs, still on RAL under /mnt/ral/jnightin/euclid); superseded by euclid_dr1 (euclid_dr1_prelim defunct) per the human 2026-10-15; folder kept under Science/active and RAL active/ by human decision 2026-10-14; RAL tree moved to the category layout 2026-10-15"
 
 euclid_dr1_prelim:
   remote: none
   local_path: /mnt/c/Users/Jammy/Science/archive/euclid_dr1_prelim
-  ral_root: /mnt/ral/jnightin/euclid_dr1_prelim
+  ral_root: /mnt/ral/jnightin/archive/euclid_dr1_prelim
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, sync, status]
@@ -144,15 +158,15 @@ ep_toy_gaussian:
   note: "born 2026-09-10 as the graphical-ep campaign's confidence test on the PyAutoFit#1405 collapse toy at N=50: joint BlackJAX NUTS vs EP x3 on identical data; model and EP settings verbatim from complete/2026/07 ep_toy_diagnostic; CPU-only, data simulated in memory from its seed; remote PyAutoLabs/ep_toy_gaussian (private) created 2026-09-10"
 
 # --------------------------------------------------------------------------- #
-# dormant — git repos only. The non-git trees (subhalo, euclid_group, z_*) are
+# dormant — git repos only. The non-git trees (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 (subhalo, non-git, is the one exception: registered active 2026-10-15). `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/archive/profiling
-  ral_root: /mnt/ral/jnightin/profiling
+  ral_root: /mnt/ral/jnightin/archive/profiling
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -166,7 +180,7 @@ profiling:
 cowls_diana:
   remote: none
   local_path: /mnt/c/Users/Jammy/Science/archive/cowls_diana
-  ral_root: /mnt/ral/jnightin/cowls_diana
+  ral_root: /mnt/ral/jnightin/archive/cowls_diana
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -180,7 +194,7 @@ cowls_diana:
 subhalo_simulations:
   remote: none
   local_path: /mnt/c/Users/Jammy/Science/archive/subhalo_simulations
-  ral_root: /mnt/ral/jnightin/subhalo_simulations
+  ral_root: /mnt/ral/jnightin/archive/subhalo_simulations
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -194,7 +208,7 @@ subhalo_simulations:
 slope_hierarchy:
   remote: Jammy2211/slope_hierarchy
   local_path: /mnt/c/Users/Jammy/Science/complete/slope_hierarchy
-  ral_root: /mnt/ral/jnightin/slope_hierarchy
+  ral_root: /mnt/ral/jnightin/complete/slope_hierarchy
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -208,7 +222,7 @@ slope_hierarchy:
 slope_hierarchy_scale:
   remote: PyAutoLabs/slope_hierarchy_scale
   local_path: /mnt/c/Users/Jammy/Science/active/slope_hierarchy_scale
-  ral_root: /mnt/ral/jnightin/slope_hierarchy_scale
+  ral_root: /mnt/ral/jnightin/active/slope_hierarchy_scale
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, sync, status, submit, push-submit, jobs, tail, check]
@@ -222,7 +236,7 @@ slope_hierarchy_scale:
 pj011646:
   remote: Jammy2211/PJ011646
   local_path: /mnt/c/Users/Jammy/Science/archive/PJ011646
-  ral_root: /mnt/ral/jnightin/z_vault/PJ011646
+  ral_root: /mnt/ral/jnightin/archive/PJ011646
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -236,7 +250,7 @@ pj011646:
 concr:
   remote: Jammy2211/cosmology_and_cancer
   local_path: /mnt/c/Users/Jammy/Science/archive/concr
-  ral_root: /mnt/ral/jnightin/concr
+  ral_root: /mnt/ral/jnightin/archive/concr
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull]
@@ -250,7 +264,7 @@ concr:
 ic50_workspace:
   remote: Jammy2211/ic50_workspace
   local_path: /mnt/c/Users/Jammy/Science/active/ic50_workspace
-  ral_root: /mnt/ral/jnightin/ic50_workspace
+  ral_root: /mnt/ral/jnightin/active/ic50_workspace
   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]
@@ -264,7 +278,7 @@ ic50_workspace:
 autolens_inference:
   remote: PyAutoLabs/autolens_inference
   local_path: /home/jammy/Code/PyAutoLabs/lens/autolens_inference
-  ral_root: /mnt/ral/jnightin/autolens_inference
+  ral_root: /mnt/ral/jnightin/inference/autolens_inference
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
@@ -278,7 +292,7 @@ autolens_inference:
 autofit_inference:
   remote: PyAutoLabs/autofit_inference
   local_path: /home/jammy/Code/PyAutoLabs/fit/autofit_inference
-  ral_root: /mnt/ral/jnightin/autofit_inference
+  ral_root: /mnt/ral/jnightin/inference/autofit_inference
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
@@ -306,7 +320,7 @@ euclid_sersics:
 pj011646_final:
   remote: none
   local_path: /mnt/c/Users/Jammy/Science/complete/PJ011646_final
-  ral_root: /mnt/ral/jnightin/PJ011646_final
+  ral_root: /mnt/ral/jnightin/complete/PJ011646_final
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, logs, status, submit, jobs, sacct, tail, du, check]

projects/euclid.md

@@ -1,16 +1,17 @@
-# euclid — The original Euclid DR1 grade-AB catalogue project, superseded by euclid_dr1_prelim
+# euclid — The original Euclid DR1 grade-AB catalogue project, superseded by euclid_dr1
 
 Project: euclid
 Issue: none
 
 ## Now
 
-Dormant since 2026-09-07: superseded by euclid_dr1_prelim. Three questions were planned and never run (see the archive).
+Dormant: superseded by euclid_dr1 (euclid_dr1_prelim is defunct). The tree is kept under Science/active and RAL `active/euclid` (category layout, 2026-10-15); no question is open.
 
 ## Runs
 
 ## Log
 
+- 2026-10-15 — note — superseded by euclid_dr1 (euclid_dr1_prelim defunct) per the human; stays dormant; folder under Science/active and RAL active/; ral_root repointed to the category layout (PyAutoCortex#67)
 - 2026-08-28 — note — question: Do we recover Sersic indices or is prior pile-up artefact — planned, never run [archive/tasks/euclid/sersic_index_recovery.md]
 - 2026-08-28 — note — question: Can a fitted Euclid lens be resimulated and recovered — planned, never run [archive/tasks/euclid/resimulate_fitted_lens_simulator.md]
 - 2026-08-28 — note — question: How robust are magnification estimates under model match and mismatch — planned, never run [archive/tasks/euclid/magnification_robustness.md]

projects/subhalo.md

@@ -0,0 +1,14 @@
+# subhalo — SLaM subhalo modelling of the SLACS lens sample
+
+Project: subhalo
+Issue: none
+
+## Now
+
+Registered 2026-10-15 (PyAutoCortex#67): SLACS sample under dataset/, output/ empty, no runs yet; ral_root not yet created on RAL — the first hpc/sync push creates it.
+
+## Runs
+
+## Log
+
+- 2026-10-15 — note — ledger opened