chore(deps): bump the claw-cargo-minor-patch group across 1 directory with 3 updates

Bumps the claw-cargo-minor-patch group with 3 updates in the /1-Distributed-Systems/agents/claw/rust directory: [serde_json](https://github.com/serde-rs/json), [regex](https://github.com/rust-lang/regex) and [pulldown-cmark](https://github.com/raphlinus/pulldown-cmark). Updates `serde_json` from 1.0.149 to 1.0.150 - [Release notes](https://github.com/serde-rs/json/releases) - [Commits](https://github.com/serde-rs/json/compare/v1.0.149...v1.0.150) Updates `regex` from 1.12.3 to 1.13.0 - [Release notes](https://github.com/rust-lang/regex/releases) - [Changelog](https://github.com/rust-lang/regex/blob/master/CHANGELOG.md) - [Commits](https://github.com/rust-lang/regex/compare/1.12.3...1.13.0) Updates `pulldown-cmark` from 0.13.3 to 0.13.4 - [Release notes](https://github.com/raphlinus/pulldown-cmark/releases) - [Commits](https://github.com/raphlinus/pulldown-cmark/compare/v0.13.3...v0.13.4) --- updated-dependencies: - dependency-name: pulldown-cmark dependency-version: 0.13.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: claw-cargo-minor-patch - dependency-name: regex dependency-version: 1.12.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: claw-cargo-minor-patch - dependency-name: serde_json dependency-version: 1.0.150 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: claw-cargo-minor-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Add module decomposition analysis
2026-07-31 03:05:21 +00:00 · 2026-07-13 15:36:34 +00:00 · 2026-07-08 07:45:01 +08:00
2 changed files with 281 additions and 8 deletions
--- a/1-Distributed-Systems/agents/claw/rust/Cargo.lock
+++ b/1-Distributed-Systems/agents/claw/rust/Cargo.lock
@ -922,9 +922,9 @@ dependencies = [

 [[package]]
 name = "pulldown-cmark"
-version = "0.13.3"
+version = "0.13.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7c3a14896dfa883796f1cb410461aef38810ea05f2b2c33c5aded3649095fdad"
+checksum = "e9f068eba8e7071c5f9511831b44f32c740d5adf574e990f946ddb53db2f314e"
 dependencies = [
 "bitflags",
 "getopts",
@ -1068,9 +1068,9 @@ dependencies = [

 [[package]]
 name = "regex"
-version = "1.12.3"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e10754a14b9137dd7b1e3e5b0493cc9171fdd105e0ab477f51b72e7f3ac0e276"
+checksum = "2a0e75113e14dc5acb068cd0786884f214f1312650a3d36d269f5c4f3cdee8a2"
 dependencies = [
 "aho-corasick",
 "memchr",
@ -1091,9 +1091,9 @@ dependencies = [

 [[package]]
 name = "regex-syntax"
-version = "0.8.10"
+version = "0.8.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc897dd8d9e8bd1ed8cdad82b5966c3e0ecae09fb1907d58efaa013543185d0a"
+checksum = "d6f6ff9a378485b298a5286656da665ba74413d36db0979633275d2e708145d4"

 [[package]]
 name = "reqwest"
@ -1334,9 +1334,9 @@ dependencies = [

 [[package]]
 name = "serde_json"
-version = "1.0.149"
+version = "1.0.150"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "83fc039473c5595ace860d8c4fafa220ff474b3fc6bfdb4293327f1a37e94d86"
+checksum = "e8014e44b4736ed0538adeecded0fce2a272f22dc9578a7eb6b2d9993c74cfb9"
 dependencies = [
 "itoa",
 "memchr",
--- 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.