Merge 86f573c3f1 into c54cf937ce

Bumps the notion-tauri-cargo-minor-patch group with 1 update in the /5-Applications/notion-native-tauri directory: [tauri](https://github.com/tauri-apps/tauri).


Updates `tauri` from 2.11.2 to 2.11.5
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-v2.11.2...tauri-v2.11.5)

Updates `tauri-build` from 2.6.2 to 2.6.3
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-build-v2.6.2...tauri-build-v2.6.3)

---
updated-dependencies:
- dependency-name: tauri
  dependency-version: 2.11.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: notion-tauri-cargo-minor-patch
- dependency-name: tauri-build
  dependency-version: 2.6.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: notion-tauri-cargo-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

5-Applications/notion-native-tauri/Cargo.lock

@@ -3004,9 +3004,9 @@ checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
 
 [[package]]
 name = "tauri"
-version = "2.11.2"
+version = "2.11.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "437404997acf375d85f1177afa7e11bb971f274ed6a7b83a2a3e339015f4cc28"
+checksum = "667b20e2726d572dea2de7370da16e188eb06008faf9a92fab7cdc46791190b5"
 dependencies = [
  "anyhow",
  "bytes",
@@ -3055,9 +3055,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-build"
-version = "2.6.2"
+version = "2.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4aa1f9055fc23919a54e4e125052bed16ed04aef0487086e758fe01a67b451c7"
+checksum = "bc9ce40b16101cb6ea63d3e221567affd1c3a9205f95d7bc574941a10636b632"
 dependencies = [
  "anyhow",
  "cargo_toml",
@@ -3076,9 +3076,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-codegen"
-version = "2.6.2"
+version = "2.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e4a0319528a025a38c4078e7dae2c446f4e63620ddb0659a643ede1cb38f90e9"
+checksum = "08279169ff42f8fc45a1dbc9dcae888893ba95288142e5880c59b93a26d2cfc5"
 dependencies = [
  "base64 0.22.1",
  "brotli",
@@ -3103,9 +3103,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-macros"
-version = "2.6.2"
+version = "2.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae6cb4e3896c21d2f6da5b31251d2faea0153bba56ed0e970f918115dbee4924"
+checksum = "e8b394794f399a421811d06966343e7933fcae92d59f5180b9388d1174497a45"
 dependencies = [
  "heck 0.5.0",
  "proc-macro2",
@@ -3117,9 +3117,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-runtime"
-version = "2.11.2"
+version = "2.11.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "48222d7116c8807eaa6fe2f372e023fae125084e61e6eca6d70b7961cdf129ef"
+checksum = "b0b4bc95aed361b0019067d189a1174a603d460d0f6c72606512d59fc9c12ec8"
 dependencies = [
  "cookie",
  "dpi",
@@ -3142,9 +3142,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-runtime-wry"
-version = "2.11.2"
+version = "2.11.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b83849ee63ecb27a8e8d0fe51915ca215076914aca43f96db1179f0f415f6cd9"
+checksum = "4e6fac707727b7a2f48e4ded90976324267371073edbb415ffb73bb0458d203f"
 dependencies = [
  "gtk",
  "http",
@@ -3168,9 +3168,9 @@ dependencies = [
 
 [[package]]
 name = "tauri-utils"
-version = "2.9.2"
+version = "2.9.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "092379df9a707631978e6c56b1bc2401d387f01e2d4a3c123360d167bbb9aa95"
+checksum = "3e176a18e67764923c4f1ce66f25ae4abe5f688384d5eb1a0fa6c77f3d90f887"
 dependencies = [
  "anyhow",
  "brotli",
@@ -3548,9 +3548,9 @@ dependencies = [
 
 [[package]]
 name = "tray-icon"
-version = "0.23.1"
+version = "0.24.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15edbb0d80583e85ee8df283410038e17314df5cba30da2087a54a85216c0773"
+checksum = "65ba1e5f6b9ef9fd87e21b9c6f351554dbd717960089168fcfdef854686961dc"
 dependencies = [
  "crossbeam-channel",
  "dirs",

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.