# Document Sets — Collated Index

**Generated:** 2026-06-29  
**Scope:** Research Stack (6-Documentation/docs) + SilverSight (docs/)  
**Total:** ~360 documents organized into 9 sets  
**Last audited:** 2026-06-30 (94.2% Lean module coverage, 93.7% Python docstring coverage, 100% receipt hash coverage)

---

## Set 1: Core Formal Mathematics

The theorem-backed foundation. Every document here maps to a Lean module with a `lake build` pass.

| Document | Location | Lean Module |
|----------|----------|-------------|
| SidonSets.lean reference | `distilled/` | `CoreFormalism.SidonSets` |
| InteractionGraphSidon | `distilled/` | `CoreFormalism.InteractionGraphSidon` |
| SieveLemmas | `distilled/` | `CoreFormalism.SieveLemmas` |
| FixedPoint arithmetic spec | `distilled/ArithmeticSpec_Corrected_2026-05-11.md` | `CoreFormalism.FixedPoint` |
| Chentsov finite reconstruction | `docs/fundamental_math/CHENTSOV_FINITE_MATH.md` | `CoreFormalism.ChentsovFinite` |
| BraidEigensolid convergence | `docs/fundamental_math/G3_EIGENSOLID_FIXED_POINT.md` | `CoreFormalism.BraidEigensolid` |
| Burgers PDE 0D braid isomorphism | `distilled/0D_genus_layer_infinity_absorption_2026-06-19.md` | `Semantics.BurgersPDE` |
| Alpha inverse derivation | `distilled/Alpha_Inverse_137_Derivation.md` | `Semantics.HCMMR` |
| AtomicResolution entropy collapse | `distilled/AtomicResolution_EntropyCollapse_2026-05-11.md` | `Semantics.HCMMR` |
| Dual quaternion math | `docs/fundamental_math/` | `CoreFormalism.BraidSpherionBridge` |
| Capability grid mapping | `docs/research/CAPABILITY_GRID_MAPPING.md` | `PanelOptimizer` (planned) |

**Path:** `6-Documentation/docs/distilled/`, `6-Documentation/docs/fundamental_math/`, `docs/fundamental_math/`

---

## Set 2: RRC Pipeline

Equation classification, alignment, and the 278-equation corpus.

| Document | Location | Lean Module |
|----------|----------|-------------|
| RRC Emit alignment gate | `formal/SilverSight/RRC/Emit.lean` | `SilverSight.RRC.Emit` |
| Q16_16Manifold corpus | `formal/SilverSight/RRC/Q16_16Manifold.lean` | `SilverSight.RRC.Q16_16Manifold` |
| ReceiptDensity scoring | `formal/SilverSight/RRC/ReceiptDensity.lean` | `SilverSight.RRC.ReceiptDensity` |
| PIST Classification | `formal/SilverSight/PIST/Classify.lean` | `SilverSight.PIST.Classify` |
| PIST Matrices250 | `formal/SilverSight/PIST/Matrices250.lean` | `SilverSight.PIST.Matrices250` |
| AVMIsa Emit (output boundary) | `formal/SilverSight/AVMIsa/Emit.lean` | `SilverSight.AVMIsa.Emit` |
| RRCLogogramProjection | `formal/SilverSight/RRCLogogramProjection.lean` | `SilverSight.RRCLogogramProjection` |
| RRC refactor readiness | `docs/RRC_REFACTOR_READINESS.md` | — |
| Project flow map | `6-Documentation/docs/pipeline/PROJECT_FLOW_MAP.md` | — |

**Path:** `formal/SilverSight/RRC/`, `formal/SilverSight/PIST/`, `formal/SilverSight/AVMIsa/`

---

## Set 3: Feasible-Set / Optimization

Constraint relaxation, QUBO, k-hot treatment, and the Burgers-Gram connection.

| Document | Location | Lean Module |
|----------|----------|-------------|
| FeasibleSet Theorem | `formal/SilverSight/FeasibleSet/Theorem.lean` | `SilverSight.FeasibleSet.Theorem` |
| QUBO k-hot treatment | `formal/SilverSight/FeasibleSet/QUBORelaxation.lean` | `SilverSight.FeasibleSet.QUBORelaxation` |
| Gram matrix reduction | `docs/research/CAPABILITY_GRID_MAPPING.md` §7 | `PanelOptimizer` (planned) |
| Burgers energy decomposition | `Semantics/BurgersPDE.lean` (comment §530) | `Semantics.BurgersPDE` |
| FFS signal analysis (ext) | `6-Documentation/docs/extensions/ffs_signal_analysis_pending.md` | — |

**Path:** `formal/SilverSight/FeasibleSet/`, `docs/research/`

---

## Set 4: Cost / Model Selection

Dual quaternion χ, financial decision engine, arbitrage, capability grid.

| Document | Location | Python/Lean |
|----------|----------|-------------|
| Dual quaternion model selector | `4-Infrastructure/shim/dual_quat_model_selector.py` | Python |
| Model panel (pluggable) | `4-Infrastructure/shim/model_panel.py` | Python |
| Cost transparency | `formal/SilverSight/CollectiveIntelligence/CostTransparency.lean` | Lean |
| Collective intelligence framework | `docs/research/COLLECTIVE_INTELLIGENCE_OPTIMIZATION.md` | — |
| Capability grid mapping | `docs/research/CAPABILITY_GRID_MAPPING.md` | — |
| Dual quat refinement plan | `6-Documentation/docs/refinement/DUAL_QUAT_MODEL_SELECTOR_REFINEMENT.md` | — |
| Transparent cost theorem | `formal/SilverSight/CollectiveIntelligence/CostTransparency.lean` | Lean |

**Path:** `4-Infrastructure/shim/`, `formal/SilverSight/CollectiveIntelligence/`

---

## Set 5: Anti-Smuggle / Rigor

Verification protocol, adversarial review, mutation testing, CAS grounding.

| Document | Location | Status |
|----------|----------|--------|
| Anti-smuggle protocol | `AGENTS.md` §"Beyond Rigorous" | ✅ Defined |
| Adversarial review (formal) | `docs/adversarial_review/ADVERSARIAL_REVIEW_FORMAL.md` | ✅ Complete |
| Adversarial review (math) | `docs/adversarial_review/ADVERSARIAL_REVIEW_MATH.md` | ✅ Complete |
| Adversarial review (code) | `docs/adversarial_review/ADVERSARIAL_REVIEW_CODE.md` | ✅ Complete |
| Adversarial review (systems) | `docs/adversarial_review/ADVERSARIAL_REVIEW_SYSTEMS.md` | ✅ Complete |
| Adversarial review (crypto) | `docs/adversarial_review/ADVERSARIAL_REVIEW_CRYPTO.md` | ✅ Complete |
| Anti-smuggle refactor plan | `docs/refactor/ANTI_SMUGGLE_REFACTOR_PLAN.md` | 📋 Planned |
| Anti-drift evidence standards | `6-Documentation/docs/AGENTS.md` §15 | ✅ Complete |
| Claim-state ladder | `6-Documentation/docs/AGENTS.md` §15.4 | ✅ Complete |
| NP-hard proof standards | `6-Documentation/docs/AGENTS.md` §15.5 | ✅ Complete |

**Path:** `docs/adversarial_review/`, `docs/refactor/`

---

## Set 6: Specs / Architecture

System specifications, protocols, and architectural documents.

| Document | Location |
|----------|----------|
| AVM canonical spec | `6-Documentation/docs/specs/AVM_CANONICAL_SPEC.md` |
| ENE schema | `6-Documentation/docs/specs/ENE_MEMORY_ATLAS_SPEC.md` |
| DP-RRC receipt encoding | `6-Documentation/docs/specs/DP_RRC_RECEIPT_ENCODING_SPEC.md` |
| FPGA morphic scalar | `6-Documentation/docs/specs/FPGA_MORPHIC_SCALAR_SPEC.md` |
| Virtio-Net compute | `6-Documentation/docs/specs/virtio_net_compute_fabric_spec.md` |
| GCCL encoding contract | `6-Documentation/docs/specs/GCCL_ENCODING_CONTRACT.md` |
| GENSIS compiler | `6-Documentation/docs/specs/GENSIS_COMPILER_SPEC.md` |
| SilverSight spec | `6-Documentation/docs/specs/SilverSight_Spec.md` |
| SMN semantic mass numbers | `6-Documentation/docs/specs/SMN_SEMANTIC_MASS_NUMBERS.md` |
| AngrySphinx spec | `6-Documentation/docs/specs/ANGRYSPHINX_DONATED_CYCLE_GATE_SPEC.md` |
| SilverSight architecture | `docs/ARCHITECTURE.md` |
| Library manifest | `docs/LIBRARY_MANIFEST.md` |
| RRC placement | `docs/RRC_PLACEMENT.md` |
| Hachimoji DNA encoding | `docs/HACHIMOJI_DNA_ENCODING.md` |

**Path:** `6-Documentation/docs/specs/`, `docs/`

---

## Set 7: Research / Speculative

Biology, neuroscience, materials science, and speculative extensions.

| Document | Location |
|----------|----------|
| Brain as Manifold | `6-Documentation/docs/BRAIN_AS_MANIFOLD.md` |
| Cancer as compression failure | `6-Documentation/docs/speculative-materials/CancerAsCompressionFailure.md` |
| DNA as game theory | `6-Documentation/docs/speculative-materials/DNA_AsGameTheory_QuantumDynamics.md` |
| Biology as PDE manifold | `6-Documentation/docs/speculative-materials/BiologyAsPDEManifold.md` |
| Neuroscience docs | `6-Documentation/docs/neuroscience/` (3 files) |
| Biomodel catalog | `6-Documentation/docs/biomechanical_model_catalog_v0_1.md` |
| Genetic benchmark review | `6-Documentation/docs/GENETIC_BENCHMARK_REVIEW_RESPONSE.md` |
| Charged mass braid sieve | `6-Documentation/docs/charged_mass_braid_sieve.md` |
| FFS signal analysis (ext) | `6-Documentation/docs/extensions/ffs_signal_analysis_pending.md` |

**Path:** `6-Documentation/docs/speculative-materials/`, `6-Documentation/docs/neuroscience/`

---

## Set 8: Project Management

Roadmaps, porting maps, work logs, build logs, plans.

| Document | Location |
|----------|----------|
| ROADMAP (authoritative) | `6-Documentation/docs/roadmaps/ROADMAP.md` |
| Forest map waterfall | `6-Documentation/docs/roadmaps/RESEARCH_STACK_FOREST_MAP_WATERFALL.md` |
| PORTING_MAP | `SilverSight/PORTING_MAP.md` |
| REBASE_RULES | `SilverSight/REBASE_RULES.md` |
| TRACEABILITY_GRAPH | `SilverSight/TRACEABILITY_GRAPH.md` |
| WORK_LOG | `SilverSight/WORK_LOG.md` |
| BREAKGLASS_LOG | `SilverSight/BREAKGLASS_LOG.md` |
| Build logs | `docs/build_logs/` (6 files) |
| SilverSight thesis triage | `6-Documentation/docs/plans/SilverSight_theorem_triage.md` |
| Completion pipeline | `6-Documentation/docs/plans/SilverSight_completion_pipeline.md` |
| Sovereign proceed plan | `6-Documentation/docs/plans/SOVEREIGN_PROCEED_PLAN_V1.md` |
| Anti-smuggle refactor plan | `docs/refactor/ANTI_SMUGGLE_REFACTOR_PLAN.md` |

**Path:** `6-Documentation/docs/roadmaps/`, `6-Documentation/docs/plans/`, `docs/build_logs/`

---

## Set 9: Papers

Publication drafts, equation papers, paper structure, publication strategy.

| Document | Location |
|----------|----------|
| OTOM v1 paper structure | `6-Documentation/docs/papers/OTOM_V1_ARXIV_READY_STRUCTURE.md` |
| OTOM v1 full paper draft | `6-Documentation/docs/papers/OTOM_V1_FULL_PAPER_STRUCTURE_INTEGRATED_DRAFT.md` |
| Publication package | `6-Documentation/docs/papers/PUBLICATION_PACKAGE.md` |
| Behavioral manifold pipeline | `6-Documentation/docs/semantics/BEHAVIORAL_MANIFOLD_PIPELINE.md` |
| Cold review formula catalog | `6-Documentation/docs/research/COLD_REVIEW_FORMULA_CATALOG.md` |
| Multi-paper strategy | `6-Documentation/docs/speculative-materials/MULTI_PAPER_PUBLICATION_STRATEGY.md` |
| Equation papers (00–10+) | `6-Documentation/docs/papers/EQUATION_*.md` (15 files) |
| Nature rigor prep | `6-Documentation/docs/semantics/NATURE_RIGOR_PREP.md` |

**Path:** `6-Documentation/docs/papers/`, `6-Documentation/docs/research/`

---

## Cross-Set Dependencies

```
Set 1 (Core Math) ──────────────────────────────────────────┐
    │                                                        │
    ├──→ Set 2 (RRC Pipeline) — uses Sidon, CRT, Q16_16      │
    ├──→ Set 3 (Optimization) — uses FixedPoint, Burgers     │
    └──→ Set 4 (Model Selection) — uses DualQuat, χ, cost    │
                                                              │
Set 5 (Anti-Smuggle) — verifies ALL other sets               │
    │                                                        │
    └──→ Set 6 (Specs) — architecture that implements        │
    └──→ Set 8 (Management) — tracks what to port/build      │
    └──→ Set 9 (Papers) — documents what to publish          │

Set 7 (Research/Speculative) — independent, no dependencies on other sets
```

---

## How to Use This Index

Each document set has a canonical path. When starting new work:

1. Check Set 8 (roadmaps, porting map) for what's planned
2. Check Set 5 (anti-smuggle) for the verification protocol
3. Find the relevant Lean module in Sets 1-4
4. Check Set 6 (specs) for architecture constraints
5. Check Set 7 (research) for any speculative connections