SilverSight/docs/DOCUMENT_SETS.md

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)

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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/

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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/

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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/

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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/

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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/

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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/

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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/

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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/

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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/

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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

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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