Merge a19b8a6701 into c54cf937ce

chore(deps): bump the root-npm-minor-patch group across 1 directory with 3 updates
Bumps the root-npm-minor-patch group with 3 updates in the / directory: [@cline/sdk](https://github.com/cline/cline/tree/HEAD/sdk/packages/sdk), [@modelcontextprotocol/inspector](https://github.com/modelcontextprotocol/inspector) and [cline](https://github.com/cline/cline/tree/HEAD/apps/cli). Updates `@cline/sdk` from 0.0.41 to 0.0.59 - [Release notes](https://github.com/cline/cline/releases) - [Changelog](https://github.com/cline/cline/blob/main/CHANGELOG.md) - [Commits](https://github.com/cline/cline/commits/sdk/sdk/v0.0.59/sdk/packages/sdk) Updates `@modelcontextprotocol/inspector` from 0.21.2 to 0.22.0 - [Release notes](https://github.com/modelcontextprotocol/inspector/releases) - [Commits](https://github.com/modelcontextprotocol/inspector/compare/0.21.2...0.22.0) Updates `cline` from 3.0.29 to 3.0.39 - [Release notes](https://github.com/cline/cline/releases) - [Changelog](https://github.com/cline/cline/blob/main/apps/cli/CHANGELOG.md) - [Commits](https://github.com/cline/cline/commits/cli-v3.0.39/apps/cli) --- updated-dependencies: - dependency-name: "@cline/sdk" dependency-version: 0.0.54 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: root-npm-minor-patch - dependency-name: "@modelcontextprotocol/inspector" dependency-version: 0.22.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: root-npm-minor-patch - dependency-name: cline dependency-version: 3.0.33 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: root-npm-minor-patch ... Signed-off-by: dependabot[bot] <support@github.com>
2026-07-31 03:05:21 +00:00 · 2026-07-13 14:46:56 +00:00 · 2026-07-13 14:46:52 +00:00 · 2026-07-08 07:45:01 +08:00
3 changed files with 522 additions and 370 deletions
--- a/MODULE_DECOMPOSITION.md
+++ b/MODULE_DECOMPOSITION.md
@ -0,0 +1,273 @@
+# Research-Stack MODULE_DECOMPOSITION.md
+
+**Date:** 2026-07-08
+**Status:** Analysis complete — 12 proposed standalone modules
+
+---
+
+## Current State
+
+- **Total .lean files:** 925 (in `0-Core-Formalism/lean/Semantics/`)
+- **Sorry count:** 76 across 29 files
+- **Foundation:** `Semantics.FixedPoint` imported by 452 files
+- **Second layer:** `Semantics.Bind` imported by 71 files
+- **Third layer:** `Semantics.DynamicCanal` imported by 25 files
+- **Current lakefile:** `lakefile.toml` (monolithic, all roots in one target)
+
+---
+
+## Proposed Module Groups (12 modules)
+
+### Module 1: `rs_core` — Foundation Axioms
+**Files:** 3 | **Sorry:** 19 | **External deps:** Mathlib (Manifold, Probability, Analysis)
+
+| File | Path |
+|------|------|
+| BindAxioms | Core/ |
+| InformationManifold | Core/ |
+| T1_Coherence | Core/ |
+
+**Internal deps:** None (this is the root)
+**Notes:** 19 sorrys in T1_Coherence (12) and InformationManifold (7). These are the "brain" — the SIM framework axioms. T1_Coherence v2.0 replaced vacuous `True := by trivial` with honest `sorry`.
+
+---
+
+### Module 2: `rs_numerics` — Fixed-Point & Q16_16 Arithmetic
+**Files:** ~15 | **Sorry:** 0 | **External deps:** Mathlib (Data.Nat, Data.Int, Data.Real)
+
+Core files (imported by 452+ others):
+- FixedPoint (the single most imported file)
+- Q16_16Numerics
+- Toolkit
+- PhysicsScalarBridge
+- RegimeCore
+
+**Internal deps:** rs_core (BindAxioms)
+**Notes:** This is the true foundation — almost everything imports FixedPoint. Must be extracted first.
+
+---
+
+### Module 3: `rs_bind` — Bind Infrastructure
+**Files:** ~20 | **Sorry:** 0 | **External deps:** Lean.Data.Json, Mathlib
+
+Core files:
+- Bind (imported by 71 files)
+- DynamicCanal (imported by 25 files)
+- LocalDerivative
+- OrthogonalAmmr
+- ManifoldStructures
+
+**Internal deps:** rs_core, rs_numerics
+**Notes:** Bind and DynamicCanal are the infrastructure layer that most domain modules depend on.
+
+---
+
+### Module 4: `rs_braid` — Braid Theory
+**Files:** ~13 | **Sorry:** 0 | **External deps:** Mathlib
+
+Files (prefix `Braid*`):
+- BraidBracket, BraidStrand, BraidCross, BraidField, BraidStateN
+- BraidEigensolid, BraidSpherionBridge
+- + related files
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Self-contained cluster with 22 internal imports. Clear boundary.
+
+---
+
+### Module 5: `rs_physics` — Physics & Conservation Laws
+**Files:** ~30 | **Sorry:** 1 | **External deps:** Mathlib (Analysis, Topology)
+
+Subdirectories: `Physics/` (24), `PhysicsData/` (1), `FNWH/` (4)
+Key files:
+- Conservation, Boundary, Interaction, Projection
+- BurgersBridge, BurgersPDE
+- DESIInvariant, DESIModelProjection
+- NBody, QCLEnergy, RydbergExperimentalTest
+- LHCb_BToKStarMuMu (real LHCb data!)
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Contains actual experimental data references (LHCb). The BurgersPDE files are imported by 13 others.
+
+---
+
+### Module 6: `rs_extensions` — Biological & Ecological Extensions
+**Files:** 105 | **Sorry:** 0 | **External deps:** Mathlib (Analysis, SpecialFunctions)
+
+All files in `Semantics/Extensions/`:
+- Biological laws (70+ files: BioComplexSystems, CellularGrowthLaws, etc.)
+- Ecological dynamics (EcologicalBehaviors, EcologicalNetworkDynamics, etc.)
+- Evolutionary dynamics (EvolutionaryLandscapeDynamics, etc.)
+- Cognitive/social dynamics (CognitiveLearningDynamics, SocialCognitiveDynamics, etc.)
+- Physics-adjacent (HarmonicKinkPlasmaManifold, HyperbolicStateSurface, etc.)
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Largest module (105 files). Could be further split into Bio/Ecology/Evolution/Cognitive sub-modules. Zero sorrys — these are all statement-only (axiom/theorem definitions without proof obligations).
+
+---
+
+### Module 7: `rs_hcmmr` — HCMMR Laws & Kernels
+**Files:** 20 | **Sorry:** 0 | **External deps:** Mathlib
+
+All in `Semantics/HCMMR/`:
+- Law14 through Law21 (Motion, SignalDetection, Field, Entropy, Observer, etc.)
+- Kernels: HyperEigenSpectrum, BoundaryEigenFire, etc.
+- FAMMScarMemory, SNRAnomalyDetector, PrimeGearCache
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Self-contained law framework. Clear naming convention (Law##).
+
+---
+
+### Module 8: `rs_hardware` — Hardware & FPGA
+**Files:** 12 | **Sorry:** 0 | **External deps:** None (hardware-level)
+
+All in `Semantics/Hardware/`:
+- AdaptiveFabric, AgenticHardware, BitstreamWitness
+- Blitter6502OISC (OISC computer!)
+- EmergencyBootShell/State/Types
+- HardwareExtraction, LaserPathCell
+- TangNano9K/ (3 files — actual FPGA target)
+- NIICore, RGFlowFAMM
+
+**Internal deps:** rs_numerics
+**Notes:** Contains TangNano9K FPGA code. Self-contained hardware layer.
+
+---
+
+### Module 9: `rs_nii` — NIICore Cognitive Architecture
+**Files:** 20 | **Sorry:** 0 | **External deps:** Mathlib
+
+All in `Semantics/NIICore/`:
+- CognitiveLoadIntegration, DifferentialAttentionMorphing
+- HierarchicalController, MetaLearning
+- MorphicCoreId, MorphicFieldCategory, MorphingTriggers
+- SemanticAnalysis, SemanticCapabilitySystem, SemanticRGFlow
+- UncertaintyQuantification, Verification, etc.
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Self-contained cognitive architecture. Clear internal naming.
+
+---
+
+### Module 10: `rs_genomic` — Genomic Compression
+**Files:** 6 | **Sorry:** 0 | **External deps:** Mathlib
+
+All in `Semantics/GenomicCompression/`:
+- Components, Compression, Field, NonDriftProof, Theorems, Types
+
+Plus `Semantics/Biology/` (3 files):
+- BioRxivFormalization, QuaternionGenomic, RGFlowBioinformatics
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Small, focused module. NonDriftProof name suggests drift-prevention guarantees.
+
+---
+
+### Module 11: `rs_testing` — Tests & Benchmarks
+**Files:** ~45 | **Sorry:** 0 | **External deps:** Mathlib
+
+- `Semantics/Testing/` (39 files): adversarial, baseline, conservation, GPU, benchmark tests
+- `Semantics/Benchmarks/` (2 files): Grid17x17, HadwigerNelson
+- `Semantics/Toybox/` (4 files): HierarchicalBinding, ObserverAngle, etc.
+
+**Internal deps:** rs_numerics (FixedPointTest, etc.)
+**Notes:** Test infrastructure. Should be buildable but not imported by other modules.
+
+---
+
+### Module 12: `rs_scaffold` — Extension Scaffold
+**Files:** 36 | **Sorry:** 1 | **External deps:** Mathlib
+
+All in `ExtensionScaffold/`:
+- **Compression/** (14 files): AdaptiveBlock, CellCore, CodingCost, HutterContext, etc.
+- **Temporal/** (9 files): CommitClock, MetabolicTvi, OMT, RegenerationPolicy, etc.
+- **ENE/** (5 files): SemanticLinter, SessionArchive, AutoImported, etc.
+- **Physics/** (2 files): NBody, VideoWeirdMachine
+- **Topology/** (2 files): PlasmaTopology, Wormhole
+- **Thermodynamics/** (1 file): ThroatPhysics
+- **Decoherence/** (1 file): HistoryTvi
+- **Seed/** (1 file): uSeed
+- MissingProofsTest (1 file)
+
+**Internal deps:** rs_numerics, rs_bind
+**Notes:** Already well-organized by subdirectory. Compression/ is the densest cluster.
+
+---
+
+## Orphan / Unclassified Files
+
+These files in `Semantics/` (flat) don't clearly belong to any cluster:
+
+| File | Imports | Notes |
+|------|---------|-------|
+| SSMS | FixedPoint | Standalone |
+| ShellModel | FixedPoint | Standalone |
+| Canon | FixedPoint | Standalone |
+| GoldenSpiral | FixedPoint | Standalone |
+| CollatzBraid | FixedPoint | Standalone |
+| Various `test_native_decide` | None | Test file |
+
+**Recommendation:** These go into rs_numerics or a rs_misc catch-all.
+
+---
+
+## Dependency Graph
+
+```
+rs_core (3 files, 19 sorrys)
+  └─► rs_numerics (~15 files, 0 sorrys)
+       ├─► rs_bind (~20 files)
+       │    ├─► rs_braid (~13 files)
+       │    ├─► rs_physics (~30 files)
+       │    ├─► rs_extensions (105 files)
+       │    ├─► rs_hcmmr (20 files)
+       │    ├─► rs_hardware (12 files)
+       │    ├─► rs_nii (20 files)
+       │    ├─► rs_genomic (9 files)
+       │    └─► rs_scaffold (36 files)
+       └─► rs_testing (~45 files) [leaf, not imported by others]
+```
+
+---
+
+## Sorry Distribution
+
+| Module | Files | Sorry Count | Files with Sorry |
+|--------|-------|-------------|-----------------|
+| rs_core | 3 | 19 | 2 |
+| rs_numerics | ~15 | 0 | 0 |
+| rs_bind | ~20 | 0 | 0 |
+| rs_braid | ~13 | 0 | 0 |
+| rs_physics | ~30 | 1 | 1 |
+| rs_extensions | 105 | 0 | 0 |
+| rs_hcmmr | 20 | 0 | 0 |
+| rs_hardware | 12 | 0 | 0 |
+| rs_nii | 20 | 0 | 0 |
+| rs_genomic | 9 | 0 | 0 |
+| rs_testing | ~45 | 0 | 0 |
+| rs_scaffold | 36 | 1 | 1 |
+| **Total** | **~328** | **21** | **4** |
+
+**Note:** 55 sorrys are in the flat `Semantics/` directory files not yet assigned to modules. The 76 total sorry count includes files that need further classification.
+
+---
+
+## Recommended Extraction Order
+
+1. **rs_numerics** first (FixedPoint is imported by 452 files — everything depends on it)
+2. **rs_core** second (BindAxioms → InformationManifold → T1_Coherence)
+3. **rs_bind** third (Bind + DynamicCanal)
+4. **rs_braid** fourth (clear cluster, easy to extract)
+5. **rs_testing** fifth (leaf module, no downstream deps)
+6. **rs_scaffold** sixth (already organized by subdirectory)
+7. Remaining modules in any order (rs_physics, rs_extensions, rs_hcmmr, rs_hardware, rs_nii, rs_genomic)
+
+---
+
+## Open Questions
+
+1. **Should rs_extensions (105 files) be split further?** Bio/Ecology/Evolution/Cognitive are distinct domains.
+2. **What to do with the 513 flat Semantics/ files?** Many are standalone statements (axiom/theorem). Need per-file import analysis to assign to modules.
+3. **Should sorrys be addressed before or after extraction?** Extracting first makes the sorry boundaries visible.
+4. **The flat Semantics/ files contain ~55 sorrys** — these need classification before final module assignment.
--- a/package-lock.json
+++ b/package-lock.json
@ -6,11 +6,11 @@
    "": {
      "name": "research-stack",
      "dependencies": {
-        "@cline/sdk": "^0.0.41",
-        "@modelcontextprotocol/inspector": "^0.21.2",
+        "@cline/sdk": "^0.0.59",
+        "@modelcontextprotocol/inspector": "^0.22.0",
        "@modelcontextprotocol/sdk": "^1.29.0",
        "better-sqlite3": "^12.10.0",
-        "cline": "^3.0.7"
+        "cline": "^3.0.39"
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    },
    "node_modules/@ai-sdk/amazon-bedrock": {
@ -775,13 +775,13 @@
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      "dependencies": {
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-        "@cline/shared": "0.0.41",
+        "@cline/llms": "0.0.59",
+        "@cline/shared": "0.0.59",
        "nanoid": "^5.1.7"
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      "engines": {
@ -789,9 +789,9 @@
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@ -804,9 +804,9 @@
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+      "resolved": "https://registry.npmjs.org/@cline/cli-darwin-x64/-/cli-darwin-x64-3.0.39.tgz",
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@ -819,9 +819,9 @@
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@ -834,9 +834,9 @@
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@ -849,9 +849,9 @@
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@ -864,9 +864,9 @@
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@ -879,13 +879,13 @@
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-      "resolved": "https://registry.npmjs.org/@cline/core/-/core-0.0.41.tgz",
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+      "resolved": "https://registry.npmjs.org/@cline/core/-/core-0.0.59.tgz",
+      "integrity": "sha512-3k1L1xxasYqircqjKPGyIj2HWdW6fdq4QEUeCt2YEcRIEdJ9BqrVuCKahKJiyHCbQU/jDQ3XmgAcQ0NsU+1J/Q==",
      "dependencies": {
-        "@cline/agents": "0.0.41",
-        "@cline/llms": "0.0.41",
-        "@cline/shared": "0.0.41",
+        "@cline/agents": "0.0.59",
+        "@cline/llms": "0.0.59",
+        "@cline/shared": "0.0.59",
        "@modelcontextprotocol/sdk": "^1.29.0",
        "@opentelemetry/api": "^1.9.0",
        "@opentelemetry/api-logs": "^0.214.0",
@ -898,22 +898,30 @@
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        "@opentelemetry/sdk-trace-node": "^2.6.1",
        "@opentelemetry/semantic-conventions": "^1.40.0",
-        "jiti": "^1.21.7",
+        "jiti": "^2.7.0",
        "nanoid": "^5.1.7",
        "node-machine-id": "^1.1.12",
-        "simple-git": "^3.32.3",
+        "simple-git": "3.36.0",
        "ws": "^8.20.0",
        "yaml": "^2.8.2",
        "zod": "^4.3.6"
      },
      "engines": {
        "node": ">=22"
+      },
+      "peerDependencies": {
+        "posthog-node": "^5.8.0"
+      },
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+        "posthog-node": {
+          "optional": true
+        }
      }
    },
    "node_modules/@cline/llms": {
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+      "resolved": "https://registry.npmjs.org/@cline/llms/-/llms-0.0.59.tgz",
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@ -924,7 +932,8 @@
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        "@ai-sdk/provider": "^3.0.8",
        "@aws-sdk/credential-providers": "^3.922.0",
-        "@cline/shared": "0.0.41",
+        "@cline/shared": "0.0.59",
+        "@jerome-benoit/sap-ai-provider": "4.6.9",
        "@langfuse/otel": "^4.0.0",
        "@opentelemetry/api": "^1.9.0",
        "@opentelemetry/sdk-trace-node": "^2.6.1",
@ -950,21 +959,21 @@
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-      "dependencies": {
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-        "zod": "^4.3.6",
-        "zod-to-json-schema": "^3.25.1"
-      },
-      "engines": {
-        "node": ">=22"
-      }
-    },
-    "node_modules/cline/node_modules/jiti": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/jiti/-/jiti-2.7.0.tgz",
-      "integrity": "sha512-AC/7JofJvZGrrneWNaEnJeOLUx+JlGt7tNa0wZiRPT4MY1wmfKjt2+6O2p2uz2+skll8OZZmJMNqeke7kKbNgQ==",
-      "license": "MIT",
-      "bin": {
-        "jiti": "lib/jiti-cli.mjs"
+        "@cline/cli-darwin-arm64": "3.0.39",
+        "@cline/cli-darwin-x64": "3.0.39",
+        "@cline/cli-linux-arm64": "3.0.39",
+        "@cline/cli-linux-x64": "3.0.39",
+        "@cline/cli-windows-arm64": "3.0.39",
+        "@cline/cli-windows-x64": "3.0.39"
      }
    },
    "node_modules/cliui": {
@ -5291,12 +5170,12 @@
      "license": "ISC"
    },
    "node_modules/jiti": {
-      "version": "1.21.7",
-      "resolved": "https://registry.npmjs.org/jiti/-/jiti-1.21.7.tgz",
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+      "version": "2.7.0",
+      "resolved": "https://registry.npmjs.org/jiti/-/jiti-2.7.0.tgz",
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      "license": "MIT",
      "bin": {
-        "jiti": "bin/jiti.js"
+        "jiti": "lib/jiti-cli.mjs"
      }
    },
    "node_modules/jks-js": {
--- a/package.json
+++ b/package.json
@ -11,11 +11,11 @@
    "probe-science": "sh -c 'if [ -x .venv-science/bin/python ]; then .venv-science/bin/python scripts/probe_science_toolbelt.py; else python3 scripts/probe_science_toolbelt.py; fi'"
  },
  "dependencies": {
-    "@cline/sdk": "^0.0.41",
-    "@modelcontextprotocol/inspector": "^0.21.2",
+    "@cline/sdk": "^0.0.59",
+    "@modelcontextprotocol/inspector": "^0.22.0",
    "@modelcontextprotocol/sdk": "^1.29.0",
    "better-sqlite3": "^12.10.0",
-    "cline": "^3.0.7"
+    "cline": "^3.0.39"
  },
  "overrides": {
    "@openai/codex": "0.132.0"