S214/V170: Deep Debt Evolution Sprint — registry alignment, IPC error typing, Rust idioms

Registry alignment: 6 pipeline capabilities (eigensolve, digester_anderson_coupling,
isomorphic_reservoir, wdm_ensemble_qs, introgression_nn, attention_anderson) now
advertised via capability.list (39→45). Hardcoded "skunkbat" literal → primal_names
constant. Discovery standardized on canonical capability.list with dual-probe fallback.
Feature gate cleanup: 4 redundant #[cfg(feature = "barracuda")] removed from lib.rs-
gated modules. IPC helpers evolved from Result<_,String> to Result<_,IpcError>. Silent
IPC fallback now logged via log::warn!. HashMap insert chains → iterator collect,
O(n²) Vec dedup → HashSet, inter_population_af_variance generalized to AsRef<[f64]>.
B3/B4 paper queue synced to COMPLETE. 754 tests, zero regressions.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: ecoPrimal

CHANGELOG.md

@@ -5,7 +5,18 @@ All notable changes to neuralSpring are documented here.
 Format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 This project uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] — 2026-05-19 (Sessions 203–213: Tier 2 convergence + niche atomic + Wave 17 + deep debt + doc evolution + Wave 20 + live composition + deep debt 6th + GPU parity + lithoSpore audit + B3/B4 ML surrogates)
+## [Unreleased] — 2026-05-22 (Sessions 203–214: Tier 2 convergence + niche atomic + Wave 17 + deep debt + doc evolution + Wave 20 + live composition + deep debt 6th + GPU parity + lithoSpore audit + B3/B4 ML surrogates + deep debt evolution sprint)
+
+### 2026-05-22 — Session S214 (Deep Debt Evolution Sprint)
+
+- **Registry alignment** — 6 pipeline capabilities (`science.eigensolve`, `science.digester_anderson_coupling`, `science.isomorphic_reservoir`, `science.wdm_ensemble_qs`, `science.introgression_nn`, `science.attention_anderson`) now advertised via `capability.list`. Previously exercised in NUCLEUS dispatch but never registered. 45 capabilities (39 → 45).
+- **Hardcode elimination** — `"skunkbat"` string literal in `handlers.rs` replaced with `primal_names::SKUNKBAT` constant. Zero hardcoded primal names remaining.
+- **Discovery standardization** — `probe_capabilities()` now uses canonical `capability.list` with dual-probe fallback to `capabilities.list` (plural) for older primals. IPC discovery doc updated to describe hint-then-probe model.
+- **Feature gate cleanup** — Documented `composed` feature alias in `Cargo.toml`. Removed 4 redundant `#[cfg(feature = "barracuda")]` annotations and dead `#[cfg(not(feature = "barracuda"))]` fallback branches in `loss_landscape.rs` and `weight_spectral/metrics.rs` (modules already gated at `lib.rs` level).
+- **IPC error typing** — `validation/composition.rs` IPC helpers evolved from `Result<_, String>` to `Result<_, IpcError>` with structured `Transport`/`Protocol` variants. Silent IPC fallback in `executor.rs` now logs via `log::warn!`.
+- **Rust idiom improvements** — 12 `HashMap::insert` chains in `dispatch.rs` converted to `[].into_iter().collect()`. O(n²) `Vec::contains` dedup in `discovered_primals()` replaced with `HashSet`. `inter_population_af_variance` generalized from `&[Vec<f64>]` to `&[impl AsRef<[f64]>]`, eliminating unnecessary `to_vec()` allocation in CPU fallback.
+- **Paper queue sync** — B3 (Good 2017) and B4 (Blount 2008) status updated from QUEUED to COMPLETE in `PAPER_REVIEW_QUEUE.md`.
+- **Test count** — 754 tests, zero regressions.
 
 ### 2026-05-19 — Session S213 (B3/B4 ML Surrogates for lithoSpore Modules 3+4)
 

CONTROL_EXPERIMENT_STATUS.md

@@ -1,6 +1,6 @@
 # neuralSpring — Control Experiment Status
 
-**Last updated**: May 19, 2026 (Session S213 — B3/B4 ML Surrogates. 10 validation scenarios. 39 capabilities. 754 workspace tests. V169 handoff.)
+**Last updated**: May 22, 2026 (Session S214 — B3/B4 ML Surrogates. 10 validation scenarios. 45 capabilities. 754 workspace tests. V170 handoff.)
 **Gate**: Eastgate (i9-12900K, 32 GB DDR5, RTX 4070 12 GB + TITAN V 12 GB NVK, Pop!_OS 22.04)
 **Python**: 3.10.12, PyTorch 2.9.0+cu128, NumPy 2.2.6, SciPy 1.15.3
 **Rust**: Edition 2024 (MSRV 1.87), clippy pedantic + nursery, unsafe_code=forbid

Cargo.toml

@@ -85,8 +85,12 @@ default = []
 # barraCuda library linking — enables GPU validation, tensor ops, and all
 # barracuda-dependent modules.
 barracuda = ["dep:barracuda", "dep:neural-spring-forge", "dep:wgpu"]
+# JSON-RPC primal binary dependencies (CLI, async runtime, RPC framework).
 primal = ["anyhow", "clap", "env_logger", "tarpc"]
+# Semantic alias: primal with biomeOS composition context. Currently
+# equivalent to `primal`; will diverge when composition-specific deps land.
 composed = ["primal"]
+# guideStone certification: primal + primalSpring ecoPrimal integration.
 guidestone = ["primalspring", "primal"]
 
 [dev-dependencies]

EVOLUTION_READINESS.md

@@ -1,6 +1,6 @@
 # neuralSpring — Evolution Readiness
 
-**Date**: May 19, 2026 (Session S213 — B3/B4 ML Surrogates for lithoSpore modules 3+4. LSTM+HMM+ESN allele classifier (Good 2017) + ESN citrate early-warning (Blount 2008). 10 validation scenarios. 39 capabilities. 754 workspace tests (IPC-first) + 19 certification. V169 handoff)
+**Date**: May 22, 2026 (Session S214 — B3/B4 ML Surrogates for lithoSpore modules 3+4. LSTM+HMM+ESN allele classifier (Good 2017) + ESN citrate early-warning (Blount 2008). 10 validation scenarios. 45 capabilities. 754 workspace tests (IPC-first) + 19 certification. V170 handoff)
 **barraCuda**: v0.4.0 (`../../primals/barraCuda/crates/barracuda`). 806+ WGSL shaders, wgpu 28, Sprint 2 APIs (activations, rng, tridiagonal_ql), healthSpring domain, batched logsumexp, CoralReefDevice. `PrecisionRoutingAdvice` with `F64NativeNoSharedMem` Ada Lovelace reclassification, `WORKGROUP_SIZE_1D` constant, cross-spring provenance registry, `BatchedOdeRK45F64`, `mean_variance_to_buffer`, coralReef Phase 10 IPC. Three-tier precision: F32/F64/Df64 (lean 3-tier model, F16+templates removed). Deep debt: typed errors, named constants, `Arc<str>` hot-path, `RwLock` compiler, ring buffer back-off, streaming pipeline completion.
 **ToadStool**: S146+ at `751b3849`. Hardware testing, PCIe transport, ResourceOrchestrator, 19,900+ tests. Absorbed neuralSpring `pipeline_graph` DAG + hotSpring `streaming_dispatch`. Dual-write discovery (canonical + coralReef-compatible). `GpuDevice` enrichment (render_node, driver, arch). `gpu.dispatch` + `shader.compile` + `orchestration` capabilities. Compute triangle unblocked. Deep debt, zero-copy.
 **coralReef**: Iteration 49. `coral-glowplug` crate (sovereign PCIe broker), GV100 per-runlist registers, HBM2 training, bar cartography, 1842+ tests. Sovereign shader compiler (WGSL → native GPU binary). NVIDIA SM70-SM89, AMD RDNA2+ (E2E GPU dispatch verified on RDNA2). Three-tier precision architecture: f32 native, f64 DFMA+polynomial lowering, df64 preamble auto-prepend. `Fp64Strategy` in `CompileOptions`. Built-in `df64_preamble.wgsl`. 8 neuralSpring shaders in corpus.

README.md

@@ -1,6 +1,6 @@
 # neuralSpring — Learning, Surrogates, and Isomorphic Patterns
 
-**Last updated**: May 19, 2026 (Session S213 — B3/B4 ML Surrogates: LSTM+HMM+ESN allele trajectory classifier (Good 2017, 100% accuracy) + ESN citrate early-warning (Blount 2008, 94.3% accuracy) for lithoSpore modules 3+4. 39 capabilities, 10 scenarios, 754 tests. V169 handoff).
+**Last updated**: May 22, 2026 (Session S214 — Deep Debt Evolution Sprint: registry alignment (39→45 capabilities), IPC error typing, discovery standardization, feature gate cleanup, Rust idiom improvements. 45 capabilities, 10 scenarios, 754 tests. V170).
 
 **The learning layer: ML surrogates, transfer learning, scholarly reproduction, and the shared computational DNA across domains.**
 

config/capability_registry.toml

@@ -104,6 +104,38 @@ method = "science.ltee_citrate_esn"
 description = "B4 ESN citrate early-warning classifier (Blount 2008, lithoSpore Module 4)"
 stability = "evolving"
 
+# ── science.* pipeline stages (NUCLEUS composition graph) ──
+
+[capabilities.eigensolve]
+method = "science.eigensolve"
+description = "Eigendecomposition via Householder QR (spectral pipeline root stage)"
+stability = "stable"
+
+[capabilities.digester_anderson_coupling]
+method = "science.digester_anderson_coupling"
+description = "Digester-Anderson disorder coupling (bioprocess × spectral)"
+stability = "stable"
+
+[capabilities.isomorphic_reservoir]
+method = "science.isomorphic_reservoir"
+description = "Isomorphic ESN reservoir spectral analysis across domains"
+stability = "stable"
+
+[capabilities.wdm_ensemble_qs]
+method = "science.wdm_ensemble_qs"
+description = "WDM ensemble quorum sensing (disorder × game theory)"
+stability = "stable"
+
+[capabilities.introgression_nn]
+method = "science.introgression_nn"
+description = "HMM introgression detection on neural network weight layers"
+stability = "stable"
+
+[capabilities.attention_anderson]
+method = "science.attention_anderson"
+description = "Attention mechanism spectral analysis (Anderson localization in transformers)"
+stability = "stable"
+
 # ── health.* (upstream stable — primalSpring canonical) ──
 
 [capabilities.health_liveness]

docs/PRIMAL_GAPS.md

@@ -5,9 +5,9 @@
 > Living gap log for neuralSpring's proto-nucleate composition.
 > Reviewed against `primalSpring/graphs/downstream/downstream_manifest.toml` neuralspring entry.
 >
-> **Date:** 2026-05-17 | **Spring version:** 0.1.0 | **primalSpring:** v0.9.25 (Wave 35, 445 methods)
-> **Session:** S213 — B3/B4 ML Surrogates: implemented LSTM+HMM+ESN allele trajectory classifier (B3, Good 2017) and ESN citrate early-warning (B4, Blount 2008) for lithoSpore modules 3+4. 39 capabilities, 32 checks (B3: 16/16, B4: 16/16). Pipeline integration, capability registry wired.
-> Prior: S212 lithoSpore Audit Absorption, S211 GPU Parity + Compute Dispatch, S210 deep debt 6th pass, S209 live composition, S208 Wave 20 schema.
+> **Date:** 2026-05-22 | **Spring version:** 0.1.0 | **primalSpring:** Wave 38 (445 methods)
+> **Session:** S214 — Deep Debt Evolution Sprint: 6 pipeline capabilities advertised (39→45), IPC error typing evolved to `IpcError`, discovery standardized on `capability.list` with dual-probe fallback, redundant feature gates removed, HashMap insert chains → iterator collect, O(n²) dedup → HashSet, silent IPC fallback logging added. Zero regressions, 754 tests.
+> Prior: S213 B3/B4 ML Surrogates, S212 lithoSpore Audit Absorption, S211 GPU Parity + Compute Dispatch, S210 deep debt 6th pass, S209 live composition.
 
 ---
 

experiments/README.md

@@ -1,6 +1,6 @@
 # neuralSpring — Experiment Journal
 
-**Current state (Session S213)**: 754 workspace tests (IPC-first) + 19 certification tests (guidestone L5). 68+ modules, 269 binaries, 521+ `.rs` files, 0 clippy, 0 unsafe, 0 `#[allow()]`, 0 production panics, 0 TODO/FIXME/HACK. Wave 17+20 signal API (`primal.announce` + `nest.store` + `nest.commit` + `node.compute`). 39 capabilities (stability tiers annotated), 10 validation scenarios, 7 IPC modules. Live composition via `execute_graph_live()`. 6/6 science pipeline stages GPU-dispatchable (GpuOnly + GpuPreferred). Degradation behavior documented. Trio semantics reviewed. 27/27 papers reproduced, 397/397 Python baselines, 20 bench scripts across 15 domains. Deep debt zero-debt (6 audits: S199, S202c, S204b, S205b, S207b, S210). Edition 2024. MSRV 1.87. barraCuda v0.4.0. V169 handoff. May 19, 2026.
+**Current state (Session S214)**: 754 workspace tests (IPC-first) + 19 certification tests (guidestone L5). 68+ modules, 269 binaries, 521+ `.rs` files, 0 clippy, 0 unsafe, 0 `#[allow()]`, 0 production panics, 0 TODO/FIXME/HACK. Wave 17+20 signal API (`primal.announce` + `nest.store` + `nest.commit` + `node.compute`). 45 capabilities (stability tiers annotated), 10 validation scenarios, 7 IPC modules. Live composition via `execute_graph_live()`. 6/6 science pipeline stages GPU-dispatchable (GpuOnly + GpuPreferred). Degradation behavior documented. Trio semantics reviewed. 27/27 papers reproduced, 397/397 Python baselines, 20 bench scripts across 15 domains. Deep debt zero-debt (6 audits: S199, S202c, S204b, S205b, S207b, S210). Edition 2024. MSRV 1.87. barraCuda v0.4.0. V170 handoff. May 22, 2026.
 
 ### Session S193 — 2026-05-09 (Interstadial Eukaryotic Evolution)
 

experiments/results/gap-status.json

@@ -1,8 +1,8 @@
 {
   "spring": "neuralSpring",
-  "session": "S213",
-  "date": "2026-05-19",
-  "audit_response": "S213: B3/B4 ML Surrogates for lithoSpore modules 3+4. LSTM+HMM+ESN allele trajectory (Good 2017, 100% test accuracy) + ESN citrate early-warning (Blount 2008, 94.3%). 39 capabilities, 754 tests. V169 handoff.",
+  "session": "S214",
+  "date": "2026-05-22",
+  "audit_response": "S214: Deep Debt Evolution Sprint. Registry alignment (39→45 capabilities), IPC error typing (Result<_,String> → IpcError), discovery standardization (capability.list dual-probe), feature gate cleanup (4 redundant gates removed), Rust idiom improvements (HashMap chains → iterator collect, HashSet dedup, generalized inter_population_af_variance). 45 capabilities, 754 tests. V170.",
   "summary": {
     "total_main_gaps": 28,
     "resolved_main": 28,
@@ -43,7 +43,7 @@
     {"id": 25, "title": "Degradation Behavior Documentation", "status": "resolved", "resolution": "S212: docs/DEGRADATION_BEHAVIOR.md — per-primal, GPU-dependent, trio partial completion"},
     {"id": 26, "title": "Cross-Tier Parity — GPU as Parity", "status": "resolved", "resolution": "S212: GPU parity framed as substrate-level cross-tier parity (CPU=Tier2a, GPU=Tier2b)"},
     {"id": 27, "title": "Trio Transaction Semantics Review", "status": "resolved", "resolution": "S212: provenance_dispatch.rs doc comments updated with trio semantics annotations"},
-    {"id": 28, "title": "B3/B4 ML Surrogates for lithoSpore", "status": "resolved", "resolution": "S213: B3 LSTM+HMM+ESN allele classifier (16/16, 100%) + B4 ESN citrate early-warning (16/16, 94.3%). Pipeline integrated, 39 capabilities."}
+    {"id": 28, "title": "B3/B4 ML Surrogates for lithoSpore", "status": "resolved", "resolution": "S213: B3 LSTM+HMM+ESN allele classifier (16/16, 100%) + B4 ESN citrate early-warning (16/16, 94.3%). Pipeline integrated. S214: 45 capabilities (39→45)."}
   ],
   "resolved_appendix": [
     {"id": "R1", "title": "Binary Name Reconciliation", "session": "S178"},

graphs/neuralspring_deploy.toml

@@ -19,7 +19,7 @@
 # Fragments: tower_atomic, node_atomic, nest_atomic, meta_tier (superset of proto-nucleate)
 # Bonding:   Metallic (InternalNucleus, UDS-only, BTSP at Tower)
 #
-# STATUS: V169 / S213 (May 19, 2026) — B3/B4 ML surrogates for lithoSpore modules 3+4
+# STATUS: V170 / S214 (May 22, 2026) — Deep Debt Evolution Sprint: registry alignment (45 capabilities), IPC error typing, Rust idioms
 # Run: biomeos deploy graphs/neuralspring_deploy.toml
 #      biomeos niche deploy neuralspring-science
 
@@ -29,7 +29,7 @@ description = "neuralSpring ML/spectral science + inference provider atop NUCLEU
 coordination = "Sequential"
 
 [graph.metadata]
-neuralspring_version = "S213"
+neuralspring_version = "S214"
 domain = "science"
 target_node = "eastgate"
 composition_model = "nucleated"