S180: composition evolution — deployment triad, MCP parity, upstream reconciliation

Primal surface: health.check, identity.get, mcp.tools.list handlers wired.
Iterative multi-prefix method normalization (neuralspring./neural-spring./neural_spring.).
MCP tool definitions expanded 19→27 (provenance.*, primal.*, capability.list, compute.offload).
Deploy graph V130 with nest_atomic fragment.
primalSpring graphs reconciled (binary name, health method, capability set).
plasmidBin metadata refreshed (30 capabilities, correct version/domain).
Docs aligned to S180 across README, CONTEXT, specs, whitePaper, baseCamp, experiments,
CHANGELOG, EVOLUTION_READINESS, DEPRECATION_MIGRATION, CONTROL_EXPERIMENT_STATUS.
Four-layer validation chain: Python→Rust→NUCLEUS→Primal.
V130 handoff + ecosystem handoff for primal/spring teams.
1,378 tests, 264 binaries, 505 .rs files. 0 clippy, 0 fmt, 0 doc warnings.

Made-with: Cursor

Author: ecoPrimal

CHANGELOG.md

@@ -5,7 +5,22 @@ 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] — 2026-04-11 (Session 179: S179/V129 status alignment; Session 178: Composition Validation Phase, Three-Layer Stack)
+## [Unreleased] — 2026-04-11 (Session 180: Composition Evolution, Deployment Triad, MCP Parity, Upstream Reconciliation)
+
+### 2026-04-11 — Session S180 (Composition evolution: deployment triad, identity, MCP, upstream reconciliation)
+
+- **Deployment health triad**: `health.check` handler — combined liveness + readiness for benchScale/plasmidBin smoke tests (DEPLOYMENT_VALIDATION_STANDARD)
+- **T4 discovery**: `identity.get` handler — primal name, niche, version, domain, license, full capability list (ECOSYSTEM_COMPLIANCE_MATRIX)
+- **MCP tool listing**: `mcp.tools.list` on primal JSON-RPC surface — returns all 27 capabilities as discoverable tools with domain parsed from `domain.verb`
+- **MCP tool parity**: `playGround/src/mcp_tools.rs` expanded 19 → 27 definitions (added `provenance.begin`, `provenance.record`, `provenance.complete`, `provenance.status`, `primal.forward`, `primal.discover`, `capability.list`, `compute.offload`)
+- **Method normalization**: Iterative multi-prefix strip (`neuralspring.`, `neural-spring.`, `neural_spring.`) per SPRING_COMPOSITION_PATTERNS §1
+- **Deploy graph V130/S180**: Added `nest_atomic` fragment, `health.check`, `identity.get`, `mcp.tools.list` capabilities
+- **primalSpring graph reconciliation**: `neuralspring_inference_pipeline.toml` binary name fix + health method fix; `spring_deploy/neuralspring_deploy.toml` binary name + capability set alignment
+- **plasmidBin metadata refresh**: version 0.7.0→0.1.0, domain ml→science.learning, 2 stale capabilities → 30-capability surface, UniBin modes aligned
+- **Clippy fix**: `#[expect(clippy::unwrap_used)]` on forge `coralreef_bridge.rs` test (`unwrap_err` in known-Err assertion)
+- **PRIMAL_GAPS.md**: R5 (MCP parity), R6 (deployment triad), R7 (fragment alignment), R8 (upstream graph reconciliation), R9 (plasmidBin metadata), R10 (method normalization breadth)
+- **Ecosystem handoff**: `NEURALSPRING_V130_PRIMAL_COMPOSITION_PATTERNS_HANDOFF_APR11_2026.md` — patterns for primal + spring teams
+- **1,378 tests** (1,225 lib + 73 forge + 80 playGround), 264 binaries, 505 `.rs` files, 0 clippy, 0 fmt, 0 doc warnings
 
 ### 2026-04-11 — Session S179 (Deploy graph proto-nucleate alignment, composition validation execution)
 

CONTEXT.md

@@ -14,7 +14,7 @@ neuralSpring is a **spring** (niche validation domain), **not** a primal. It val
 - **Language:** Rust 2024 edition, `rust-version` **1.87**
 - **License:** AGPL-3.0-or-later (scyBorg: AGPL code + ORC mechanics + CC-BY-SA creative)
 - **Workspace:** 3 crates — `neural-spring` (library), `neural-spring-forge`, `neuralspring-playground`
-- **Scale:** 466 Rust source files; every file under 1000 lines
+- **Scale:** 505 Rust source files; every file under 1000 lines
 - **Safety:** zero `unsafe` (`#![forbid(unsafe_code)]` workspace-wide); cast lints (`cast_possible_truncation`, `cast_sign_loss`) denied
 - **Linting:** Clippy pedantic + nursery, zero warnings, zero `#[allow()]`
 - **Dependencies:** `barracuda` (math engine, `default-features = false`), `wgpu` **28** (GPU), `tokio` (async), `tarpc` (optional RPC for the primal binary), `thiserror` (typed errors: `GpuError`, `TensorError`, `ParseError`)
@@ -28,16 +28,17 @@ neuralSpring is a **spring** (niche validation domain), **not** a primal. It val
 
 ## Key Capabilities (JSON-RPC)
 
-Sixteen capabilities (`domain.verb`) when composed in biomeOS. Method naming follows Semantic Method Naming v2.1: discovery may list or resolve these via `capabilities.list` (canonical), `capability.list` (legacy), or `primal.capabilities` (alias).
+Thirty capabilities (`domain.verb`) when composed in biomeOS. Method naming follows Semantic Method Naming v2.1: discovery may list or resolve these via `capability.list` (canonical), `identity.get` (T4 discovery), or `mcp.tools.list` (MCP adapter).
 
-- `science.spectral_analysis`, `science.anderson_localization`, `science.hessian_eigen`, `science.agent_coordination`
-- `science.ipr`, `science.disorder_sweep`, `science.training_trajectory`, `science.evoformer_block`, `science.structure_module`
-- `science.folding_health`, `science.gpu_dispatch`, `science.cross_spring_provenance`, `science.cross_spring_benchmark`, `science.precision_routing`
-- `health.liveness`, `health.readiness`
+- **Science (14):** `science.spectral_analysis`, `science.anderson_localization`, `science.hessian_eigen`, `science.agent_coordination`, `science.ipr`, `science.disorder_sweep`, `science.training_trajectory`, `science.evoformer_block`, `science.structure_module`, `science.folding_health`, `science.gpu_dispatch`, `science.cross_spring_provenance`, `science.cross_spring_benchmark`, `science.precision_routing`
+- **Health (3):** `health.liveness`, `health.readiness`, `health.check`
+- **Inference (3):** `inference.complete`, `inference.embed`, `inference.models`
+- **Provenance (4):** `provenance.begin`, `provenance.record`, `provenance.complete`, `provenance.status`
+- **Routing (6):** `primal.forward`, `primal.discover`, `capability.list`, `identity.get`, `mcp.tools.list`, `compute.offload`
 
 ## Test Coverage
 
-CI-enforced **≥90%** line coverage (`llvm-cov`). ~1,400 tests (1,211 lib + 73 forge + 80 playGround + 12 integration + 25 tokio). Suite includes unit tests, property tests, determinism tests, doc tests, integration tests, and provenance integrity tests. `ValidationSink` for machine-readable CI output (JSON, NDJSON, collecting).
+CI-enforced **≥90%** line coverage (`llvm-cov`). ~1,378 tests (1,225 lib + 73 forge + 80 playGround). Suite includes unit tests, property tests, determinism tests, doc tests, integration tests, and provenance integrity tests. `ValidationSink` for machine-readable CI output (JSON, NDJSON, collecting).
 
 ## What This Does NOT Do
 
@@ -55,7 +56,8 @@ CI-enforced **≥90%** line coverage (`llvm-cov`). ~1,400 tests (1,211 lib + 73
 ## Evolution Path
 
 ```text
-Python baseline (control/) → Rust validation (src/) → GPU (WGSL via barraCuda) → sovereign pipeline
+Python baseline (control/) → Rust validation (src/) → GPU (WGSL via barraCuda)
+  → NUCLEUS composition (primal IPC via biomeOS) → sovereign deployment
 ```
 
 ## Design Philosophy

CONTROL_EXPERIMENT_STATUS.md

@@ -1,6 +1,6 @@
 # neuralSpring — Control Experiment Status
 
-**Last updated**: April 11, 2026 (Session S179 — Composition validation phase: Python→Rust→NUCLEUS. Composition validators wired to validate_all with exit-2 honest skip. ~1,403+ tests: 1,225 lib + 73 forge + 80 playGround + 12 integration + 25 tokio. 264 binaries (261 science/GPU + 3 composition), 518 `.rs` files. 0 warnings. Cast lints denied. barraCuda v0.3.11.)
+**Last updated**: April 11, 2026 (Session S180 — Composition evolution: deployment triad, MCP parity, upstream reconciliation. 1,378 tests: 1,225 lib + 73 forge + 80 playGround. 264 binaries (241 validate + 18 bench + 5 other), 505 `.rs` files. 0 warnings. Cast lints denied. barraCuda v0.3.11.)
 **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

DEPRECATION_MIGRATION.md

@@ -1,8 +1,8 @@
 # neuralSpring — Deprecation & Migration Guide
 
-**Date**: April 10, 2026 (Sessions 44–179)
+**Date**: April 11, 2026 (Sessions 44–180)
 **barraCuda**: v0.3.11 (path dep, `default-features = false`). ToadStool S146+, coralReef Iter 49.
-**Status**: Migration complete — deprecated modules fossilized, gpu_dispatch active (47 ops, ~97% GPU). 264 binaries, ~1,392 tests (1,225 lib + 73 forge + 80 playGround + 14 integration), 0 clippy (pedantic+nursery+cast deny), 0 fmt diffs. `#![forbid(unsafe_code)]` workspace-wide, zero `#[allow()]`, zero production mocks, zero C deps. NUCLEUS composition validation layer. V129 handoff.
+**Status**: Migration complete — deprecated modules fossilized, gpu_dispatch active (47 ops, ~97% GPU). 264 binaries, 1,378 tests (1,225 lib + 73 forge + 80 playGround), 0 clippy (pedantic+nursery+cast deny), 0 fmt diffs. `#![forbid(unsafe_code)]` workspace-wide, zero `#[allow()]`, zero production mocks, zero C deps. NUCLEUS composition evolution. V130 handoff.
 **S130**: `PrecisionRoutingAdvice` wired, fused GPU regression gated, coralNAK→coralReef rename.
 **S121**: `MlpLayer` struct removed from `wdm_surrogate.rs` and `wdm_transport.rs` — replaced by `barracuda::nn::SimpleMlp` with `DenseLayer` format. `hmm_viterbi_chain_gpu` per-step f32 Tensor loop replaced by single f64 `barracuda::ops::bio::hmm_viterbi` dispatch.
 

EVOLUTION_READINESS.md

@@ -1,11 +1,12 @@
 # neuralSpring — Evolution Readiness
 
-**Date**: April 11, 2026 (Session S179 — Composition validation execution: deploy graph aligned to proto-nucleate, capability surface reconciled, three-layer validation stack complete. ~1,403+ tests: 1,225 lib + 73 forge + 80 playGround + 14 integration + 25 tokio, 264 binaries, 518 `.rs` files, 68 modules, 232+ named tolerances, 26 capabilities, 3 composition validators)
+**Date**: April 11, 2026 (Session S180 — Composition evolution: deployment health triad, T4 identity, MCP tool listing, upstream reconciliation. 1,378 tests: 1,225 lib + 73 forge + 80 playGround. 264 binaries, 505 `.rs` files, 68 modules, 232+ named tolerances, 27 capabilities, 3 composition validators)
 **barraCuda**: v0.3.11 (`../../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. **Known issue**: `enable f64;` in WGSL triggers PTXAS silent-zero regression on Ada Lovelace — fix implemented locally in `pipeline_cache.rs`, pending upstream absorption.
 **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.
-**neuralSpring**: ~1,403 tests (1,225 lib + 73 forge + 80 playGround + 12 integration + 25 tokio), 264 binaries, 518 `.rs` files, 68 modules, 0 clippy warnings (pedantic+nursery+cast deny, workspace-wide), 0 fmt diffs, 0 doctest failures. All 3 crate roots `forbid(unsafe_code)`. All files ≤1000 LOC (largest: 879 LOC). AGPL-3.0-or-later. **Zero C dependencies** (ecoBin compliant). **Rust Edition 2024**. proptest 14 invariants. **Zero `#[allow()]` workspace-wide**. ecoBin CI (musl+ARM cross-compile). `PROVENANCE_REGISTRY` (49 records, 12 tests). `OnceLock` GPU probe cache. Cast lint deny. `PRIMAL_DOMAIN`. `ValidationSink` pattern (5 sinks, 12 tests). 4 provenance integrity tests. IPC resilience wired (RetryPolicy+CircuitBreaker in live PetalTongue path). **26 capabilities** registered (ALL_CAPABILITIES = niche::CAPABILITIES). Deploy graph V129 aligned to proto-nucleate (coralReef, barraCuda, Squirrel, full capability surface).
-**S179**: Composition validation execution — deploy graph proto-nucleate alignment. Added coralReef (`shader.compile.wgsl`), barraCuda (`math.tensor`), Squirrel (`ai.query`) germination nodes to `neuralspring_deploy.toml`. BearDog `by_capability` updated to `security` (proto-nucleate alignment). ToadStool updated to `compute.dispatch.submit`, NestGate to `storage.retrieve`. `capabilities_provided` expanded from 14 science-only to full 26-capability niche surface (inference.*, health.*, provenance.*, capability.list, compute.offload, primal.*). Graph metadata: `composition_model = "nucleated"`, `bond_type = "Metallic"`, `trust_model = "InternalNucleus"`, `fragments`, `proto_nucleate` reference. `config::ALL_CAPABILITIES` expanded 18→26 to match `niche::CAPABILITIES` (single source of truth). `operation_dependencies()` and `cost_estimates()` now cover all 26 capabilities. Fixed doctest (`GpuCapabilities` import ordering). `ANDERSON_MULTIAGENT_ENVIRONMENT` pinned precisely (`Python 3.12.3, NumPy 2.2.6`). Kokkos benchmark provenance reclassified from PLACEHOLDER to ESTIMATED. `PRIMAL_GAPS.md` updated: R3 (deploy graph alignment) and R4 (capability surface reconciliation) resolved. 0 clippy warnings, 0 fmt diffs, 0 doctest failures, 1,225 lib tests PASS. Deploy graph V129/S179. V129 handoff.
+**neuralSpring**: 1,378 tests (1,225 lib + 73 forge + 80 playGround), 264 binaries, 505 `.rs` files, 68 modules, 0 clippy warnings (pedantic+nursery+cast deny, workspace-wide), 0 fmt diffs, 0 doctest failures. All 3 crate roots `forbid(unsafe_code)`. All files ≤1000 LOC (largest: 879 LOC). AGPL-3.0-or-later. **Zero C dependencies** (ecoBin compliant). **Rust Edition 2024**. proptest 14 invariants. **Zero `#[allow()]` workspace-wide**. ecoBin CI (musl+ARM cross-compile). `PROVENANCE_REGISTRY` (49 records, 12 tests). `OnceLock` GPU probe cache. Cast lint deny. `PRIMAL_DOMAIN`. `ValidationSink` pattern (5 sinks, 12 tests). 4 provenance integrity tests. IPC resilience wired (RetryPolicy+CircuitBreaker in live PetalTongue path). **27 capabilities** registered (ALL_CAPABILITIES). Deploy graph V130 aligned to proto-nucleate with `nest_atomic`. Full deployment standard: health triad, identity.get, mcp.tools.list.
+**S180**: Composition evolution — deployment health triad (`health.check`), T4 discovery (`identity.get`), MCP tool listing (`mcp.tools.list`) on primal surface. Iterative multi-prefix method normalization. MCP tool parity 27/27. Deploy graph V130 with `nest_atomic` fragment. primalSpring pipeline + deploy graph reconciled (binary name, health method, capability set). plasmidBin metadata refreshed (30 capabilities, correct version/domain). Clippy fix (forge `coralreef_bridge.rs`). PRIMAL_GAPS.md R5–R10 resolved. Ecosystem handoff crafted. 1,378 tests, 264 binaries, 505 `.rs` files. V130 handoff.
+**S179**: Composition validation execution — deploy graph proto-nucleate alignment, capability surface expanded to 26, `ALL_CAPABILITIES` reconciled with niche, PRIMAL_GAPS.md R3/R4 resolved. Deploy graph V129/S179. V129 handoff.
 **S178**: Composition validation phase — Python→Rust→NUCLEUS three-layer validation stack. `validate_all` wired with 3 composition validators (`validate_nucleus_composition`, `validate_inference_composition`, `validate_primal_discovery`) and exit-2 honest skip handling. `docs/PRIMAL_GAPS.md` reconciled with actual source (inference.* wip not open, binary naming resolved). Version strings aligned to barraCuda v0.3.11 across all specs. Deploy graph V128/S178. EVOLUTION_READINESS primal IPC wiring status added. 264 binaries, 518 `.rs` files, 1,225 lib tests. V128 handoff.
 **S176**: Deep audit execution — clippy zero-warning gate restored (6 test errors), provenance environment centralization (19 literals → 2 constants), IPC resilience wired into PetalTonguePushClient, GPU module refactor (gpu.rs → gpu/mod.rs + gpu/tests.rs), integration tests 9→12 (49/49 provenance), doc reconciliation. V126 handoff.
 **S175**: Ecosystem absorption — `ValidationSink` (StdoutSink, JsonSink, NdjsonSink, CollectingSink, SilentSink), `cast_possible_truncation`/`cast_sign_loss` deny, 4 provenance integrity tests, deploy graph V124/S174, leverage guide refresh. V125 handoff.

README.md

@@ -1,6 +1,6 @@
 # neuralSpring — Learning, Surrogates, and Isomorphic Patterns
 
-**Last updated**: April 11, 2026 (Session S179 — Composition validation phase: Python→Rust→NUCLEUS three-layer validation stack, composition validators wired to validate_all with exit-2 honest skip, PRIMAL_GAPS.md reconciled, version strings aligned to barraCuda v0.3.11, deploy graph V129/S179, primal IPC wiring status documented).
+**Last updated**: April 11, 2026 (Session S180 — Composition evolution: deployment health triad, identity.get, mcp.tools.list, iterative method normalization, MCP tool parity (27/27), deploy graph V130/S180 with nest_atomic, primalSpring + plasmidBin graph and metadata reconciliation, upstream capability set alignment).
 
 **The learning layer: ML surrogates, transfer learning, scholarly reproduction, and the shared computational DNA across domains.**
 
@@ -46,7 +46,11 @@ neuralSpring validates these primitives in Python, then hands off to the BarraCU
 
 ## Current Status: 397/397 Python PASS + 4500+ Rust+GPU PASS = **4900+ total validation checks**
 
-**S177: NUCLEUS composition validation — proto-nucleate graph validator (`validate_nucleus_composition`), inference chain validator (`validate_inference_composition`), capability-based discovery validator (`validate_primal_discovery`), bonding policy (Metallic/InternalNucleus), composition infrastructure (`validation::composition` — 5-tier socket discovery, JSON-RPC probes, honest skip exit 2), `inference.*` capability wiring (niche, config, handlers, rpc_service, MCP tools), ecoBin harvest script (`scripts/harvest_ecobin.sh`), CI composition-validation job. ~1,392 tests, 264 binaries, 518 `.rs` files. V127 handoff.**
+**S180: Composition evolution — deployment health triad (`health.check`), T4 discovery (`identity.get`), MCP tool listing on primal surface (`mcp.tools.list`), iterative multi-prefix method normalization, 27/27 MCP tool definitions, deploy graph `nest_atomic` fragment, primalSpring graph reconciliation (binary name, health method, capability set), plasmidBin metadata refresh (30 capabilities, correct version/domain). 1,378 tests, 264 binaries, 505 `.rs` files. V130 handoff.**
+
+**S179: Composition validation — PRIMAL_GAPS.md reconciled (10 gaps, 4 resolved), deploy graph V129/S179, capability surface expanded to 26 entries, version strings aligned to barraCuda v0.3.11, primal IPC wiring status documented.**
+
+**S177–S178: NUCLEUS composition validation — proto-nucleate graph validator (`validate_nucleus_composition`), inference chain validator (`validate_inference_composition`), capability-based discovery validator (`validate_primal_discovery`), bonding policy (Metallic/InternalNucleus), composition infrastructure (`validation::composition` — 5-tier socket discovery, JSON-RPC probes, honest skip exit 2), `inference.*` capability wiring (niche, config, handlers, rpc_service, MCP tools), ecoBin harvest script (`scripts/harvest_ecobin.sh`), CI composition-validation job. V127–V128 handoffs.**
 
 **S176: Deep audit execution — clippy zero-warning gate restored, provenance environment centralization (20 literals → 2 named constants), IPC resilience wired (RetryPolicy + CircuitBreaker into PetalTongue), GPU module refactor (gpu.rs → gpu/mod.rs + gpu/tests.rs), integration tests expanded (9 → 12, full 49/49 provenance coverage), doc reconciliation. ~1,403 tests, 261 binaries, 466 `.rs` files. V126 handoff.**