Research-Stack/6-Documentation/wiki/Home.md

Research Stack Wiki

Entry Points

Document	Purpose
docs/AGENTS.md	Strict LLM operating rules — the one file every agent must read first
docs/VOCABULARY_LOCK.md	Fixed terminology — Lean references, PIST/FAMM/GWL signatures
docs/GLOSSARY.md	Project-wide glossary — all terms across all domains
wiki/Concept-Archive.md	Concept archive — canonical, speculative, held, lossy, retired, and abandoned terms
docs/BEGINNERS_MAP.md	Narrative onboarding — what this stack is and why it exists
wiki/Build-System.md	Build system — pinned Python (3.11.15), uv integration, VSCode tasks, npm scripts
wiki/Text-to-CAD-Environment.md	Text-to-CAD environment — CAD-specific venv sequencing, build123d / OCP verification, agent contract
wiki/DeepSeek-Review-Process.md	AI-assisted mathematical review — receipt schema, two-stage pipeline, prime-gap example
docs/VISION_NORTH_STAR.md	Long-term vision — where the stack converges
docs/PHI_CENTER_REVAMP.md	Phi-centered cockpit architecture — cost/efficiency comparison root
docs/BRAIN_AS_MANIFOLD.md	Biological manifold theory — hyperbolic geometry, intelligence ladder, Physarum
docs/EQUATION_FOREST_INDEX.md	Equation taxonomy — kernel IDs F01–F12 and equation families
docs/MATH_MODEL_MAP.tsv	Equation registry — source of truth for all mathematical models

Specifications

Spec	Domain
docs/specs/AVM_CANONICAL_SPEC.md	Adaptive Virtual Machine — universal math language adapter
docs/specs/PHI_S3C_PIST_BRIDGE_SPEC.md	Phi–S3C–PIST bridge — witness transport for Phi-centered transforms
docs/specs/GCL_FIELD_EQUATIONS_SPEC.md	GCL field equations — manifold-weighted field snapshot
docs/specs/MS3C_NESTED_REDUCTION_GEAR_SPEC.md	Nested reduction gear — S³ shell gear reduction for AngrySphinx

Research Domains

Domain	Location
GCL / GCCL (compression language)	docs/gcl/, docs/research/GCCL_THEORY_INTRO.md
MISC / GENSIS (encoding substrates)	docs/research/MISC_THEORY.md, docs/research/MISC_GENETIC_NSPACE.md
Security / AngrySphinx	docs/research/BURGERS_READINESS_ASSESSMENT.md
FPGA / Hardware	docs/FPGA_IMPLEMENTATION_REVIEW.md, docs/FPGA_WARDEN_NODE_SPEC.md
Semantics / Lean	docs/semantics/, 0-Core-Formalism/lean/Semantics/
Safety	docs/safety/, docs/SAFETY_GATED_VERIFICATION_PLAN.md
Neuroscience	docs/neuroscience/
Physics	docs/physics/
Provenance / Audit	docs/provenance/

Roadmaps

Roadmap	Target
docs/roadmaps/UNIVERSAL_SUBSTRATE_ROADMAP.md	USTSM — 36 substrates, 7 phases, unified state machine
docs/roadmaps/RESEARCH_STACK_FOREST_MAP_WATERFALL.md	Forest map waterfall — authority and substrate plumbing

Infrastructure

Component	Location
ENE (Endless Node Edges)	4-Infrastructure/infra/ene_distributed_node.py
AVM ABI surface	avm_abi.py
AVM Core	avm_core.py
Topological Storage (Google Drive)	RcloneIntegration.lean, CONCEPTS.md §Topological Storage

Key Concept Docs

Document	Summary
CONCEPTS.md	Core concepts — FAMM, OTOM, PIST, ENE, Charged-Mass Braid Sieve
wiki/Concept-Archive.md	Full concept archive — includes abandoned/held/speculative surfaces
CITATION.cff	Terminology neutrality map — technical terms vs cultural aliases
PROJECT_MAP.md	Repository-wide directory structure and module map
MATH_MODEL_MAP.tsv	Full equation registry indexed by phinary ID

Build System & Environments

Document	Summary
wiki/Build-System.md	Python 3.11.15 pin via .python-version, uv install path, VSCode interpreter, npm script surface
wiki/Text-to-CAD-Environment.md	CAD-specific sequencing that consumes the canonical setup commands in wiki/Build-System.md
GETTING_STARTED.md	Lean toolchain installation and end-to-end Lean build walkthrough

AI-Assisted Review

Document	Summary
wiki/DeepSeek-Review-Process.md	Receipt schema (ollama_deepseek_review_receipt_v1), two-stage pipeline (deepseek-v3.2 + deepseek-v4-flash continuation), prime-gap entropy-collapse example
shared-data/artifacts/deepseek_review/	Paired answer + receipt artifacts for each review run
5-Applications/tools-scripts/llm/ollama_deepseek_review_emitter.py	Canonical Ollama-compatible DeepSeek review emitter with write-time answer-hash verification
5-Applications/tools-scripts/llm/deepseek_review_adapter.py	Related Anthropic-compatible DeepSeek adapter; it does not emit the current Ollama-style receipt schema