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Research-Stack/MODULE_DECOMPOSITION.md
allaunthefox c54cf937ce Add module decomposition analysis
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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.