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# Document Sets — Collated Index
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**Generated:** 2026-06-29
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**Scope:** Research Stack (6-Documentation/docs) + SilverSight (docs/)
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**Total:** ~360 documents organized into 9 sets
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**Last audited:** 2026-06-30 (94.2% Lean module coverage, 93.7% Python docstring coverage, 100% receipt hash coverage)
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---
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## Set 1: Core Formal Mathematics
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The theorem-backed foundation. Every document here maps to a Lean module with a `lake build` pass.
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| Document | Location | Lean Module |
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|----------|----------|-------------|
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| SidonSets.lean reference | `distilled/` | `CoreFormalism.SidonSets` |
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| InteractionGraphSidon | `distilled/` | `CoreFormalism.InteractionGraphSidon` |
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| SieveLemmas | `distilled/` | `CoreFormalism.SieveLemmas` |
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| FixedPoint arithmetic spec | `distilled/ArithmeticSpec_Corrected_2026-05-11.md` | `CoreFormalism.FixedPoint` |
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| Chentsov finite reconstruction | `docs/fundamental_math/CHENTSOV_FINITE_MATH.md` | `CoreFormalism.ChentsovFinite` |
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| BraidEigensolid convergence | `docs/fundamental_math/G3_EIGENSOLID_FIXED_POINT.md` | `CoreFormalism.BraidEigensolid` |
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| Burgers PDE 0D braid isomorphism | `distilled/0D_genus_layer_infinity_absorption_2026-06-19.md` | `Semantics.BurgersPDE` |
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| Alpha inverse derivation | `distilled/Alpha_Inverse_137_Derivation.md` | `Semantics.HCMMR` |
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| AtomicResolution entropy collapse | `distilled/AtomicResolution_EntropyCollapse_2026-05-11.md` | `Semantics.HCMMR` |
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| Dual quaternion math | `docs/fundamental_math/` | `CoreFormalism.BraidSpherionBridge` |
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| Capability grid mapping | `docs/research/CAPABILITY_GRID_MAPPING.md` | `PanelOptimizer` (planned) |
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**Path:** `6-Documentation/docs/distilled/`, `6-Documentation/docs/fundamental_math/`, `docs/fundamental_math/`
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---
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## Set 2: RRC Pipeline
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Equation classification, alignment, and the 278-equation corpus.
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| Document | Location | Lean Module |
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|----------|----------|-------------|
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| RRC Emit alignment gate | `formal/SilverSight/RRC/Emit.lean` | `SilverSight.RRC.Emit` |
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| Q16_16Manifold corpus | `formal/SilverSight/RRC/Q16_16Manifold.lean` | `SilverSight.RRC.Q16_16Manifold` |
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| ReceiptDensity scoring | `formal/SilverSight/RRC/ReceiptDensity.lean` | `SilverSight.RRC.ReceiptDensity` |
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| PIST Classification | `formal/SilverSight/PIST/Classify.lean` | `SilverSight.PIST.Classify` |
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| PIST Matrices250 | `formal/SilverSight/PIST/Matrices250.lean` | `SilverSight.PIST.Matrices250` |
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| AVMIsa Emit (output boundary) | `formal/SilverSight/AVMIsa/Emit.lean` | `SilverSight.AVMIsa.Emit` |
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| RRCLogogramProjection | `formal/SilverSight/RRCLogogramProjection.lean` | `SilverSight.RRCLogogramProjection` |
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| RRC refactor readiness | `docs/RRC_REFACTOR_READINESS.md` | — |
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| Project flow map | `6-Documentation/docs/pipeline/PROJECT_FLOW_MAP.md` | — |
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**Path:** `formal/SilverSight/RRC/`, `formal/SilverSight/PIST/`, `formal/SilverSight/AVMIsa/`
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---
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## Set 3: Feasible-Set / Optimization
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Constraint relaxation, QUBO, k-hot treatment, and the Burgers-Gram connection.
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| Document | Location | Lean Module |
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|----------|----------|-------------|
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| FeasibleSet Theorem | `formal/SilverSight/FeasibleSet/Theorem.lean` | `SilverSight.FeasibleSet.Theorem` |
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| QUBO k-hot treatment | `formal/SilverSight/FeasibleSet/QUBORelaxation.lean` | `SilverSight.FeasibleSet.QUBORelaxation` |
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| Gram matrix reduction | `docs/research/CAPABILITY_GRID_MAPPING.md` §7 | `PanelOptimizer` (planned) |
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| Burgers energy decomposition | `Semantics/BurgersPDE.lean` (comment §530) | `Semantics.BurgersPDE` |
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| FFS signal analysis (ext) | `6-Documentation/docs/extensions/ffs_signal_analysis_pending.md` | — |
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**Path:** `formal/SilverSight/FeasibleSet/`, `docs/research/`
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---
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## Set 4: Cost / Model Selection
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Dual quaternion χ, financial decision engine, arbitrage, capability grid.
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| Document | Location | Python/Lean |
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|----------|----------|-------------|
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| Dual quaternion model selector | `4-Infrastructure/shim/dual_quat_model_selector.py` | Python |
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| Model panel (pluggable) | `4-Infrastructure/shim/model_panel.py` | Python |
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| Cost transparency | `formal/SilverSight/CollectiveIntelligence/CostTransparency.lean` | Lean |
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| Collective intelligence framework | `docs/research/COLLECTIVE_INTELLIGENCE_OPTIMIZATION.md` | — |
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| Capability grid mapping | `docs/research/CAPABILITY_GRID_MAPPING.md` | — |
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| Dual quat refinement plan | `6-Documentation/docs/refinement/DUAL_QUAT_MODEL_SELECTOR_REFINEMENT.md` | — |
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| Transparent cost theorem | `formal/SilverSight/CollectiveIntelligence/CostTransparency.lean` | Lean |
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**Path:** `4-Infrastructure/shim/`, `formal/SilverSight/CollectiveIntelligence/`
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---
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## Set 5: Anti-Smuggle / Rigor
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Verification protocol, adversarial review, mutation testing, CAS grounding.
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| Document | Location | Status |
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|----------|----------|--------|
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| Anti-smuggle protocol | `AGENTS.md` §"Beyond Rigorous" | ✅ Defined |
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| Adversarial review (formal) | `docs/adversarial_review/ADVERSARIAL_REVIEW_FORMAL.md` | ✅ Complete |
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| Adversarial review (math) | `docs/adversarial_review/ADVERSARIAL_REVIEW_MATH.md` | ✅ Complete |
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| Adversarial review (code) | `docs/adversarial_review/ADVERSARIAL_REVIEW_CODE.md` | ✅ Complete |
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| Adversarial review (systems) | `docs/adversarial_review/ADVERSARIAL_REVIEW_SYSTEMS.md` | ✅ Complete |
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| Adversarial review (crypto) | `docs/adversarial_review/ADVERSARIAL_REVIEW_CRYPTO.md` | ✅ Complete |
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| Anti-smuggle refactor plan | `docs/refactor/ANTI_SMUGGLE_REFACTOR_PLAN.md` | 📋 Planned |
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| Anti-drift evidence standards | `6-Documentation/docs/AGENTS.md` §15 | ✅ Complete |
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| Claim-state ladder | `6-Documentation/docs/AGENTS.md` §15.4 | ✅ Complete |
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| NP-hard proof standards | `6-Documentation/docs/AGENTS.md` §15.5 | ✅ Complete |
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**Path:** `docs/adversarial_review/`, `docs/refactor/`
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---
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## Set 6: Specs / Architecture
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System specifications, protocols, and architectural documents.
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| Document | Location |
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|----------|----------|
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| AVM canonical spec | `6-Documentation/docs/specs/AVM_CANONICAL_SPEC.md` |
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| ENE schema | `6-Documentation/docs/specs/ENE_MEMORY_ATLAS_SPEC.md` |
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| DP-RRC receipt encoding | `6-Documentation/docs/specs/DP_RRC_RECEIPT_ENCODING_SPEC.md` |
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| FPGA morphic scalar | `6-Documentation/docs/specs/FPGA_MORPHIC_SCALAR_SPEC.md` |
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| Virtio-Net compute | `6-Documentation/docs/specs/virtio_net_compute_fabric_spec.md` |
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| GCCL encoding contract | `6-Documentation/docs/specs/GCCL_ENCODING_CONTRACT.md` |
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| GENSIS compiler | `6-Documentation/docs/specs/GENSIS_COMPILER_SPEC.md` |
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| SilverSight spec | `6-Documentation/docs/specs/SilverSight_Spec.md` |
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| SMN semantic mass numbers | `6-Documentation/docs/specs/SMN_SEMANTIC_MASS_NUMBERS.md` |
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| AngrySphinx spec | `6-Documentation/docs/specs/ANGRYSPHINX_DONATED_CYCLE_GATE_SPEC.md` |
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| SilverSight architecture | `docs/ARCHITECTURE.md` |
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| Library manifest | `docs/LIBRARY_MANIFEST.md` |
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| RRC placement | `docs/RRC_PLACEMENT.md` |
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| Hachimoji DNA encoding | `docs/HACHIMOJI_DNA_ENCODING.md` |
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**Path:** `6-Documentation/docs/specs/`, `docs/`
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---
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## Set 7: Research / Speculative
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Biology, neuroscience, materials science, and speculative extensions.
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| Document | Location |
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|----------|----------|
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| Brain as Manifold | `6-Documentation/docs/BRAIN_AS_MANIFOLD.md` |
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| Cancer as compression failure | `6-Documentation/docs/speculative-materials/CancerAsCompressionFailure.md` |
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| DNA as game theory | `6-Documentation/docs/speculative-materials/DNA_AsGameTheory_QuantumDynamics.md` |
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| Biology as PDE manifold | `6-Documentation/docs/speculative-materials/BiologyAsPDEManifold.md` |
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| Neuroscience docs | `6-Documentation/docs/neuroscience/` (3 files) |
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| Biomodel catalog | `6-Documentation/docs/biomechanical_model_catalog_v0_1.md` |
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| Genetic benchmark review | `6-Documentation/docs/GENETIC_BENCHMARK_REVIEW_RESPONSE.md` |
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| Charged mass braid sieve | `6-Documentation/docs/charged_mass_braid_sieve.md` |
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| FFS signal analysis (ext) | `6-Documentation/docs/extensions/ffs_signal_analysis_pending.md` |
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**Path:** `6-Documentation/docs/speculative-materials/`, `6-Documentation/docs/neuroscience/`
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---
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## Set 8: Project Management
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Roadmaps, porting maps, work logs, build logs, plans.
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| Document | Location |
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|----------|----------|
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| ROADMAP (authoritative) | `6-Documentation/docs/roadmaps/ROADMAP.md` |
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| Forest map waterfall | `6-Documentation/docs/roadmaps/RESEARCH_STACK_FOREST_MAP_WATERFALL.md` |
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| PORTING_MAP | `SilverSight/PORTING_MAP.md` |
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| REBASE_RULES | `SilverSight/REBASE_RULES.md` |
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| TRACEABILITY_GRAPH | `SilverSight/TRACEABILITY_GRAPH.md` |
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| WORK_LOG | `SilverSight/WORK_LOG.md` |
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| BREAKGLASS_LOG | `SilverSight/BREAKGLASS_LOG.md` |
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| Build logs | `docs/build_logs/` (6 files) |
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| SilverSight thesis triage | `6-Documentation/docs/plans/SilverSight_theorem_triage.md` |
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| Completion pipeline | `6-Documentation/docs/plans/SilverSight_completion_pipeline.md` |
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| Sovereign proceed plan | `6-Documentation/docs/plans/SOVEREIGN_PROCEED_PLAN_V1.md` |
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| Anti-smuggle refactor plan | `docs/refactor/ANTI_SMUGGLE_REFACTOR_PLAN.md` |
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**Path:** `6-Documentation/docs/roadmaps/`, `6-Documentation/docs/plans/`, `docs/build_logs/`
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---
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## Set 9: Papers
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Publication drafts, equation papers, paper structure, publication strategy.
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| Document | Location |
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|----------|----------|
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| OTOM v1 paper structure | `6-Documentation/docs/papers/OTOM_V1_ARXIV_READY_STRUCTURE.md` |
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| OTOM v1 full paper draft | `6-Documentation/docs/papers/OTOM_V1_FULL_PAPER_STRUCTURE_INTEGRATED_DRAFT.md` |
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| Publication package | `6-Documentation/docs/papers/PUBLICATION_PACKAGE.md` |
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| Behavioral manifold pipeline | `6-Documentation/docs/semantics/BEHAVIORAL_MANIFOLD_PIPELINE.md` |
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| Cold review formula catalog | `6-Documentation/docs/research/COLD_REVIEW_FORMULA_CATALOG.md` |
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| Multi-paper strategy | `6-Documentation/docs/speculative-materials/MULTI_PAPER_PUBLICATION_STRATEGY.md` |
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| Equation papers (00–10+) | `6-Documentation/docs/papers/EQUATION_*.md` (15 files) |
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| Nature rigor prep | `6-Documentation/docs/semantics/NATURE_RIGOR_PREP.md` |
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**Path:** `6-Documentation/docs/papers/`, `6-Documentation/docs/research/`
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---
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## Cross-Set Dependencies
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```
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Set 1 (Core Math) ──────────────────────────────────────────┐
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│ │
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├──→ Set 2 (RRC Pipeline) — uses Sidon, CRT, Q16_16 │
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├──→ Set 3 (Optimization) — uses FixedPoint, Burgers │
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└──→ Set 4 (Model Selection) — uses DualQuat, χ, cost │
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│
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Set 5 (Anti-Smuggle) — verifies ALL other sets │
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│ │
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└──→ Set 6 (Specs) — architecture that implements │
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└──→ Set 8 (Management) — tracks what to port/build │
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└──→ Set 9 (Papers) — documents what to publish │
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Set 7 (Research/Speculative) — independent, no dependencies on other sets
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```
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---
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## How to Use This Index
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Each document set has a canonical path. When starting new work:
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1. Check Set 8 (roadmaps, porting map) for what's planned
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2. Check Set 5 (anti-smuggle) for the verification protocol
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3. Find the relevant Lean module in Sets 1-4
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4. Check Set 6 (specs) for architecture constraints
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5. Check Set 7 (research) for any speculative connections
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