continued adding cofigs, policy, and app cleanup

Author: justinlietz93

docs/contracts/runtime-boundary-policy.yml

@@ -56,6 +56,7 @@ runtime_identity:
     - torch or GPU runtime backend
     - frontend runtime owner
     - visualization or WebSocket map-stream runtime path
+  archived_source_material:
+    - docs/sources/legacy-substrate-neurogenesis/
   legacy_exception_pending_archive:
-    - core/substrate/
     - core/global_system.py

docs/contracts/runtime-capability-coverage.yml

@@ -15,19 +15,25 @@ coverage_values:
   diagnostic_only: The source is not a runtime owner; its diagnostic goal needs a separate sparse readout decision.
 
 archival_gate:
-  rule: >
-    A source file may leave the importable runtime tree only after every
-    capability it carries is either covered, intentionally_retired, or recorded
-    as a named port with an implementation owner and acceptance gate.
+  archive_move_rule: >
+    A source file may leave the importable runtime tree when it is preserved in
+    a tracked source archive, every carried goal is recorded here, and the
+    archive README names the sparse-native port obligation.
+  deletion_rule: >
+    An archived source file may be deleted only after every capability it
+    carries is either covered or intentionally_retired with acceptance evidence.
   prohibited_inference: Static disconnection alone does not authorize deletion.
 
 capabilities:
   - id: sparse_population_change
     source_paths:
-      - core/substrate/neurogenesis.py
-      - core/substrate/growth_arbiter.py
+      - docs/sources/legacy-substrate-neurogenesis/neurogenesis.py
+      - docs/sources/legacy-substrate-neurogenesis/growth_arbiter.py
       - core/growth_arbiter.py
       - core/sie.py
+    former_runtime_paths:
+      - core/substrate/neurogenesis.py
+      - core/substrate/growth_arbiter.py
     goal: >
       Bounded node growth and culling, with cross-system state resizing and
       pressure/stability admission.
@@ -46,6 +52,8 @@ capabilities:
 
   - id: node_field_and_spike_dynamics
     source_paths:
+      - docs/sources/legacy-substrate-neurogenesis/substrate.py
+    former_runtime_paths:
       - core/substrate/substrate.py
     goal: >
       Per-node membrane state, refractory state, spike history, and discrete
@@ -61,6 +69,8 @@ capabilities:
 
   - id: intrinsic_plasticity
     source_paths:
+      - docs/sources/legacy-substrate-neurogenesis/substrate.py
+    former_runtime_paths:
       - core/substrate/substrate.py
     goal: >
       Adapt node-intrinsic parameters from recent activity while preserving
@@ -73,6 +83,8 @@ capabilities:
 
   - id: synaptic_scaling
     source_paths:
+      - docs/sources/legacy-substrate-neurogenesis/substrate.py
+    former_runtime_paths:
       - core/substrate/substrate.py
     goal: Normalize incoming excitatory support without erasing sparse structure.
     coverage: unmet
@@ -83,9 +95,11 @@ capabilities:
 
   - id: sparse_edge_pruning_and_bridge_repair
     source_paths:
-      - core/substrate/structural_homeostasis.py
+      - docs/sources/legacy-substrate-neurogenesis/structural_homeostasis.py
       - core/structural_homeostasis.py
       - core/sparse_connectome.py
+    former_runtime_paths:
+      - core/substrate/structural_homeostasis.py
     goal: Remove weak edges and repair fragmentation through bounded supported bridges.
     coverage: partial
     evidence:

docs/contracts/runtime-cleanup-classification.yml

@@ -23,8 +23,8 @@ runtime_identity:
     - core/adc.py
     - core/sie.py
     - core/sie_v2.py
-  - core/cortex/void_walkers/
-  - core/cortex/maps/
+    - core/cortex/void_walkers/
+    - core/cortex/maps/
     - core/bus.py
     - runtime/
     - io/
@@ -136,51 +136,55 @@ entries:
       - No static runtime import was found.
       - The runtime imports void_frontier_scout.FrontierScout directly.
 
-  - path: core/substrate/substrate.py
+  - path: docs/sources/legacy-substrate-neurogenesis/substrate.py
+    former_runtime_path: core/substrate/substrate.py
     class: archive
-    state: blocked_by_capability_closure
+    state: preserved_source_archive
     role: Legacy dense substrate with optional Torch/GPU backend.
     evidence:
       - Direct torch imports and a dense weight matrix are present in the source.
-      - No direct or dynamic import reference was found outside core/substrate/.
-    destination: docs/sources/legacy-substrate-neurogenesis/
-    follow_up: Do not move until node_field_and_spike_dynamics, intrinsic_plasticity, and synaptic_scaling have explicit decisions.
+      - No direct or dynamic import reference was found while the source was under core/substrate/.
+    destination: docs/sources/legacy-substrate-neurogenesis/substrate.py
+    follow_up: Do not delete until node_field_and_spike_dynamics, intrinsic_plasticity, and synaptic_scaling are covered or intentionally retired.
 
-  - path: core/substrate/neurogenesis.py
+  - path: docs/sources/legacy-substrate-neurogenesis/neurogenesis.py
+    former_runtime_path: core/substrate/neurogenesis.py
     class: archive
-    state: blocked_by_capability_closure
+    state: preserved_source_archive
     role: Legacy dense neuron-growth executor.
     evidence:
       - Imports torch and allocates a new N x N weight matrix during growth.
-      - No direct or dynamic import reference was found outside core/substrate/.
-    destination: docs/sources/legacy-substrate-neurogenesis/
-    follow_up: Do not move until sparse_population_change has a named implementation owner and acceptance gate.
+      - No direct or dynamic import reference was found while the source was under core/substrate/.
+    destination: docs/sources/legacy-substrate-neurogenesis/neurogenesis.py
+    follow_up: Do not delete until sparse_population_change is covered or intentionally retired.
 
-  - path: core/substrate/growth_arbiter.py
+  - path: docs/sources/legacy-substrate-neurogenesis/growth_arbiter.py
+    former_runtime_path: core/substrate/growth_arbiter.py
     class: archive
-    state: blocked_by_capability_closure
+    state: preserved_source_archive
     role: Legacy stability and debt-based growth decision source.
     evidence:
-      - No direct or dynamic import reference was found outside core/substrate/.
-    destination: docs/sources/legacy-substrate-neurogenesis/
+      - No direct or dynamic import reference was found while the source was under core/substrate/.
+    destination: docs/sources/legacy-substrate-neurogenesis/growth_arbiter.py
     follow_up: Archive source; do not treat its thresholds or metric names as live policy.
 
-  - path: core/substrate/structural_homeostasis.py
+  - path: docs/sources/legacy-substrate-neurogenesis/structural_homeostasis.py
+    former_runtime_path: core/substrate/structural_homeostasis.py
     class: archive
-    state: blocked_by_capability_closure
+    state: preserved_source_archive
     role: Legacy pruning and bridge-growth source.
     evidence:
-      - No direct or dynamic import reference was found outside core/substrate/.
-    destination: docs/sources/legacy-substrate-neurogenesis/
+      - No direct or dynamic import reference was found while the source was under core/substrate/.
+    destination: docs/sources/legacy-substrate-neurogenesis/structural_homeostasis.py
     follow_up: Archive source; preserve pruning and bridge-repair obligations as ports.
 
   - path: capability:sparse_neurogenesis
     class: port
     state: planned
     source_paths:
-      - core/substrate/neurogenesis.py
-      - core/substrate/growth_arbiter.py
-      - core/substrate/structural_homeostasis.py
+      - docs/sources/legacy-substrate-neurogenesis/neurogenesis.py
+      - docs/sources/legacy-substrate-neurogenesis/growth_arbiter.py
+      - docs/sources/legacy-substrate-neurogenesis/structural_homeostasis.py
     target: core/neurogenesis/
     required_invariants:
       - Bounded dynamic population growth and culling.
@@ -223,11 +227,11 @@ entries:
       - tests/guards/test_runtime_engine_prune.py guards its absence.
 
 review_notes:
-  - path: core/substrate/
+  - path: docs/sources/legacy-substrate-neurogenesis/
+    former_runtime_path: core/substrate/
     finding: Static reachability is empty, but prior boundary prose listed the package as retained.
-    resolution: Archival is blocked until each capability has a named sparse-native owner or an explicit intentional-retirement decision.
+    resolution: Source is preserved outside core/ while the sparse-native capability port remains open.
     required_before_move:
-      - Archive the source with a capability README.
       - Add a no-torch live-runtime guard.
       - Add import checks for retained sparse runtime modules.
 

docs/contracts/source-authority.yml

@@ -13,6 +13,9 @@ sources:
   aura_distinction_inventory:
     path: docs/sources/neurobiology-upgrade/Aura_Distinction_Inventory_v0.7.md
     role: atomized Aura evidence inventory
+  legacy_substrate_neurogenesis:
+    path: docs/sources/legacy-substrate-neurogenesis/
+    role: preserved source for sparse-native dynamic population and node-state ports; not live runtime code
 external_missing:
   runtime_papers:
     count_expected: 8

docs/pages/architecture/runtime-boundaries.md

@@ -50,10 +50,11 @@ The following systems have current runtime execution:
 - `core/cortex/void_walkers/`
 - `core/cortex/maps/`
 
-`SparseConnectome` is the sole live runtime substrate. The old
-`core/substrate/` package is a dense/Torch source under active archival review;
-it is not a second runtime substrate. Its dynamic-population requirements are
-preserved for the sparse-neurogenesis port, not by retaining its implementation.
+`SparseConnectome` is the sole live runtime substrate. The former
+`core/substrate/` package has moved to
+`docs/sources/legacy-substrate-neurogenesis/`; it is not a second runtime
+substrate. Its dynamic-population requirements are preserved for the
+sparse-neurogenesis port, not by retaining its implementation.
 
 `core/growth_arbiter.py`, `core/structural_homeostasis.py`, `core/void_b1.py`,
 and the optional GDSP/REVGSP adapters are retained as capability sources, not

docs/roadmap/runtime-cleanup-guardrails/ANALYSIS.md

@@ -35,9 +35,10 @@ is optional merely because its construction is not a simple top-level import.
 
 ### Legacy dense substrate
 
-The four files under `core/substrate/` have no direct import reference outside
-that directory, and no dynamic-import mechanism was found anywhere in the
-repository. Their implementation is nevertheless not disposable source:
+The four former `core/substrate/` files, now preserved under
+`docs/sources/legacy-substrate-neurogenesis/`, had no direct import reference
+outside that directory, and no dynamic-import mechanism was found anywhere in
+the repository. Their implementation is nevertheless not disposable source:
 
 - `substrate.py` imports Torch and supports a GPU backend.
 - `neurogenesis.py` imports Torch and grows by allocating a new dense `N x N`
@@ -52,8 +53,9 @@ scaling goals. The default `SparseConnectome` does not expose the corresponding
 state, and the current firing-variance signal is variance of its field `W`, not
 variance of observed firing events.
 
-The source remains an `archive` candidate, but archival is blocked. The sparse
-replacement must be derived against the requirements in
+The source is preserved in a tracked archive outside the importable runtime.
+It must not be deleted while the sparse replacement is open. That replacement
+must be derived against the requirements in
 `docs/roadmap/sparse-neurogenesis/TODO.md`, and the unowned physiology goals
 must receive either a VDM-native sparse owner or an explicit retirement record.
 
@@ -105,7 +107,7 @@ environment with all declared dependencies is exercised.
 | Surface | Class | Reason | Required next action |
 | --- | --- | --- | --- |
 | `SparseConnectome`, ADC, SIE/SIE v2, void maps/scouts, neuroplasticity | `keep` | Active runtime ownership | Add importability guards before cleanup moves. |
-| `core/substrate/` source | `archive` candidate | Statically isolated dense/Torch implementation with unclosed goals | Preserve source; do not move until coverage closes. |
+| `core/substrate/` source | `preserved archive` | Statically isolated dense/Torch implementation with unclosed goals | Keep under `docs/sources/legacy-substrate-neurogenesis/`; do not delete until coverage closes. |
 | Sparse population management | `unmet` | No fixed-size sparse executor can grow or retire nodes | Build bounded sparse/event-fed behavior. |
 | Node/spike dynamics, intrinsic plasticity, synaptic scaling | `unmet` | No compatible state or operator exists on SparseConnectome | Assign a sparse-native owner or explicitly retire each goal. |
 | `core/global_system.py` | `archive` candidate | Statically isolated ADC/SIE variant with partial successors | Close ADC and territory-conditioned-valence coverage first. |
@@ -125,6 +127,6 @@ environment with all declared dependencies is exercised.
 
 ## Next Gate
 
-Do not move source yet. First close Task 0.3: assign owners and acceptance
-gates for every unmet or unwired capability. The guard set remains necessary,
-but it protects a cleanup only after the capability obligations are explicit.
+The legacy source has moved out of the importable runtime into its tracked
+archive. Next, assign owners and acceptance gates for every unmet or unwired
+capability; the archive stays until those obligations close.

docs/roadmap/runtime-cleanup-guardrails/TODO.md

@@ -26,7 +26,7 @@ This checklist protects the fresh independent runtime identity. It is allowed to
 
 - [x] Step 0.3.1 — Add a capability-coverage contract for every current archive or port candidate.
 - [x] Step 0.3.2 — Record each goal as covered, partial, unwired, unmet, diagnostic-only, or intentionally retired.
-- [ ] Step 0.3.3 — Add a guard that prevents archival moves while capability coverage is unresolved.
+- [x] Step 0.3.3 — Add a guard that prevents deletion while capability coverage is unresolved and requires archived source preservation.
 - [ ] Step 0.3.4 — Assign an implementation owner and acceptance gate for every `unwired` or `unmet` runtime goal.
 
 ## Phase 1 — Add Hard Guard Tests
@@ -58,17 +58,17 @@ This checklist protects the fresh independent runtime identity. It is allowed to
 
 ### Task 2.1 — Move legacy substrate material out of live runtime
 
-- [ ] Step 2.1.1 — Create `docs/sources/legacy-substrate-neurogenesis/` only after Task 0.3 closes the carried capability obligations.
-- [ ] Step 2.1.2 — Move or copy old dense substrate files there as source material.
-- [ ] Step 2.1.3 — Remove the old files from live importable runtime paths.
-- [ ] Step 2.1.4 — Add `README.md` explaining that the old code is design source for sparse neurogenesis, not live runtime code.
+- [x] Step 2.1.1 — Create `docs/sources/legacy-substrate-neurogenesis/` as a tracked source archive.
+- [x] Step 2.1.2 — Move old dense substrate files there as source material.
+- [x] Step 2.1.3 — Remove the old files from live importable runtime paths.
+- [x] Step 2.1.4 — Add `README.md` explaining that the old code is design source for sparse neurogenesis, not live runtime code.
 
 ### Task 2.2 — Preserve the extracted invariant
 
-- [ ] Step 2.2.1 — Document dynamic neuron population growth as a preserved capability.
-- [ ] Step 2.2.2 — Document node-count management between configured minimum and maximum bounds.
-- [ ] Step 2.2.3 — Document growth debt, stability arbitration, seeding, culling, structural homeostasis, edge repair, and bridge growth as requirements for the sparse replacement.
-- [ ] Step 2.2.4 — Link this extraction note to `docs/roadmap/sparse-neurogenesis/TODO.md`.
+- [x] Step 2.2.1 — Document dynamic neuron population growth as a preserved capability.
+- [x] Step 2.2.2 — Document node-count management between configured minimum and maximum bounds.
+- [x] Step 2.2.3 — Document growth debt, stability arbitration, seeding, culling, structural homeostasis, edge repair, and bridge growth as requirements for the sparse replacement.
+- [x] Step 2.2.4 — Link this extraction note to `docs/roadmap/sparse-neurogenesis/TODO.md`.
 
 ## Phase 3 — Validate the Clean Runtime
 

docs/roadmap/sparse-neurogenesis/TODO.md

@@ -9,19 +9,19 @@ The legacy substrate files encode a real missing capability: dynamic self-managi
 
 ### Task 0.1 — Archive design source
 
-- [ ] Step 0.1.1 — Move old `core/substrate/` files out of live runtime path.
-- [ ] Step 0.1.2 — Preserve them under `docs/sources/legacy-substrate-neurogenesis/` or `archive/legacy-substrate-neurogenesis/`.
-- [ ] Step 0.1.3 — Add archive README explaining that these files are not runtime code.
-- [ ] Step 0.1.4 — Add guard test proving live runtime no longer imports the archived substrate path.
+- [x] Step 0.1.1 — Move old `core/substrate/` files out of live runtime path.
+- [x] Step 0.1.2 — Preserve them under `docs/sources/legacy-substrate-neurogenesis/`.
+- [x] Step 0.1.3 — Add archive README explaining that these files are not runtime code and must not be deleted before capability closure.
+- [x] Step 0.1.4 — Add guard test proving live runtime no longer imports the archived substrate path.
 
 ### Task 0.2 — Extract requirements
 
-- [ ] Step 0.2.1 — Document dynamic neuron population growth.
-- [ ] Step 0.2.2 — Document node-count management between configured minimum and maximum bounds.
-- [ ] Step 0.2.3 — Document growth debt and stability arbitration.
-- [ ] Step 0.2.4 — Document new-neuron seeding requirements.
-- [ ] Step 0.2.5 — Document culling/pruning requirements.
-- [ ] Step 0.2.6 — Document bridge growth and cluster repair requirements.
+- [x] Step 0.2.1 — Document dynamic neuron population growth.
+- [x] Step 0.2.2 — Document node-count management between configured minimum and maximum bounds.
+- [x] Step 0.2.3 — Document growth debt and stability arbitration.
+- [x] Step 0.2.4 — Document new-neuron seeding requirements.
+- [x] Step 0.2.5 — Document culling/pruning requirements.
+- [x] Step 0.2.6 — Document bridge growth and cluster repair requirements.
 
 ## Phase 1 — Define Sparse Population Policy
 

docs/sources/README.md

@@ -6,6 +6,11 @@ Current source packet:
 
 ```text
 sources/neurobiology-upgrade/
+sources/legacy-substrate-neurogenesis/
 ```
 
+The legacy substrate packet is preserved source for the sparse-native dynamic
+population port. It is not live runtime code and must not be deleted before the
+capability-coverage contract closes its carried obligations.
+
 The canonical pages under `docs/pages/` should summarize source material and point back to these files.

docs/sources/legacy-substrate-neurogenesis/README.md

@@ -0,0 +1,44 @@
+# Legacy Substrate Neurogenesis Source
+
+## Status
+
+**Archived source material. Do not delete. Do not import as live runtime
+code.**
+
+These files are the retained design source for sparse-native population work.
+They are not an alternate backend, compatibility layer, or executable fallback.
+The former implementation uses dense matrices and Torch/GPU paths that are not
+permitted in the reboot runtime.
+
+## Preserved Source
+
+- `substrate.py` - node membrane, refractory, spike-history, intrinsic
+  plasticity, and synaptic-scaling goals.
+- `neurogenesis.py` - node allocation, state extension, and initial supported
+  connection goals.
+- `growth_arbiter.py` - stability and void-debt admission goal for growth.
+- `structural_homeostasis.py` - pruning and bridge-repair goal.
+
+## Sparse-Native Obligation
+
+The active goal is dynamic `N` without dense scans or dense `N x N` allocation:
+
+- bounded growth and retirement between configured minimum and maximum counts;
+- sparse extension or retirement of adjacency, node field, stimulation,
+  territory, memory, map, SIE, and traversal state;
+- growth admission from pressure, stability, and void debt;
+- local sparse seeding, pruning, and bridge repair;
+- lifecycle events visible through the event spine; and
+- no Torch, GPU backend, optimizer, loss, gradient, or training-loop path.
+
+The implementation authority is
+`docs/roadmap/sparse-neurogenesis/TODO.md`. The capability obligations and
+current gaps are recorded in
+`docs/contracts/runtime-capability-coverage.yml`.
+
+## Archive Rule
+
+This archive exists so the original goals remain inspectable while the runtime
+is made sparse-native. A future cleanup may delete a source file only after its
+corresponding capability is covered or explicitly retired, with evidence added
+to the capability-coverage contract.