ARCHITECTURE.md — Sovereign Research Stack

The single-page map of the system. Read this first.

1. Core Idea

The Sovereign Research Stack is a formal verification and compression system grounded in cross-domain invariant analysis. Every transformation — whether a byte-compression pass, a PDE discretization step, or a spiking-neuron firing — is treated as a receipt-bearing event that must preserve declared invariants. Lean 4 is the source of truth. All computation uses Q16.16 fixed-point arithmetic. No floating-point, no unproven claims, no receipt-free promotions.

2. Layer Model

Level 6 — Meta-Computation       Cognitive Router │ Auto-Adaptive Metatyping
Level 5 — Semantic               12 Semantic Primes │ Cross-Dimensional Filter
Level 4 — Security               AngrySphinx Gate │ FAMM Frustration │ ASIC Topology
Level 3 — Thermodynamic          Trixal Quality │ Homeostatic Governor │ HyperFlow
Level 2 — Biological             Genetic Codes │ Spiking Neurons │ STDP Weights
Level 1 — Geometric              GWL 5-Factor Coupling │ Toroidal Shells │ Quaternion Torsion
Level 0 — Primordial             PIST/DIAT Shells │ Q16.16 Arithmetic │ BraidField

Level	Domain	Key Substrates	Invariant
0 (Primordial)	Pure math	PIST/DIAT shells, Q16.16, BraidField, BracketedCalculus	mass = t·(2k+1-t), arithmetic totality
1 (Geometric)	Shape-aware	GWL rotational coupling, toroidal shells, torsion quaternions, GWL throat	dE/dt ≤ 0, no zero-mass singularities
2 (Biological)	Life-aware	64 codon tables, Izhikevich spiking neurons, STDP plasticity	codon validity, spike threshold v < 30mV
3 (Thermodynamic)	Energy-aware	Trixal state (thermal/work/irreversibility), homeostatic governor, HyperFlow NS-on-shells	irreversibility < threshold,
4 (Security)	Attack-aware	AngrySphinx exponential gate, FAMM frustration tensor, ASIC admissible operations	E_solve ≥ 2^n, F > 0, operation admissibility
5 (Semantic)	Meaning-aware	CrossDimensionalFilter (12 primes), manifold networking, compression control	shared primes non-empty, flat→ordinary kernel
6 (Meta)	Self-aware	Cognitive load router, auto-adaptive metatyping (7 invariants), adaptation, SSMS_nD	efficiency ≥ 0, mass conservation across tiers

3. Three-Axis Pipeline

Substrate (ENE) ←→ Surface (Notion) ←→ Intent (Linear)
         │              │              │
         └──────────────┼──────────────┘
                        ▼
                   Metatype
                 (Q0_64 scalar)

ENE (Substrate): Holds ground truth — the SQLite-backed package store with hyperbolic concept coordinates
Notion (Surface): Human-facing UI and research database
Linear (Intent): Issue tracking and work orchestration
Metatype: The 1D Q0_64 scalar interface that every substrate reduces to, enabling cross-tier communication

4. Data Flow

Raw Data
  │
  ▼
┌──────────────────┐    PIST Remap: bytes → (shell, offset, mass) coordinates
│ PIST/DIAT Remap  │    Filter grounded bytes (mass=0), count seismic bytes
└────────┬─────────┘
         ▼
┌──────────────────┐    GWL Coupling: 5-factor similarity between token pairs
│ GWL Similarity   │    w_ij = cos(Δθ)·cos(Δφ)·(1-2|Δχ|)·exp(-|Δp|²/2σ²)
└────────┬─────────┘
         ▼
┌──────────────────┐    Cognitive Router: select optimal compression strategy
│ Cognitive Router │    L_total = λI·L_I + λE·L_E - λG·L_G + λR·L_R + λM·L_M
└────────┬─────────┘
         ▼
┌──────────────────┐    Delta GCL: variable-length delta encoding + PTOS dict + Huffman
│ Delta GCL Encode │    Q16.16 fixed-point arithmetic for all transforms
└────────┬─────────┘
         ▼
┌──────────────────┐    Trixal Verify: thermodynamic quality check
│ Trixal Verify    │    dS/dt ≤ 0, Landauer bound: W ≥ k_B·T·ln(2)
└────────┬─────────┘
         ▼
┌──────────────────┐    Homeostatic Update: surprise/regret → pressure → canal width
│ Homeostatic      │    p_{t+1} = γ·p_t + α·surprise + β·regret
└────────┬─────────┘
         ▼
   Compressed Output + Receipt

5. Seven Core Invariants

#	Invariant	Source	Domain	Statement
1	Mass Conservation	PIST	Geometry	mass = t·(2k+1−t) is preserved under all lawful transitions
2	Exponential Gate	AngrySphinx	Security	E_solve ≥ 2^n where n = type depth; NaN boundary at F=0
3	Semantic Prime Conservation	CrossDimensionalFilter	Semantics	12 irreducible primes preserved across dimensional reduction
4	Frustration Monotonicity	FAMM	Security	Triadic incompatibility → frustration grows until resolved
5	Homeostatic Fixed Point	HomeostaticGovernor	Thermodynamics	Compression pressure converges to stable p*
6	Cognitive Load Decomposition	CognitiveLoad	Meta	Strategy selection minimizes total load across 5 components
7	Q0_64 Scalar Universality	GENSIS	Meta	Every substrate state reduces to a single unsigned [0,1) scalar

6. Framework Hierarchy

GCCL = Law Stack (what must be preserved)
  │
  ├── MISC = Compression Engine (how it runs)
  │     Uses: PIST shells, GWL coupling, Cognitive Router, Trixal Verify
  │     │
  │     └── GENSIS = N-D Extension (genetic codes + hypercubic shells)
  │           Adds: 64 codon tables, Izhikevich neurons, STDP, XNA backbones
  │
  └── USTSM = Substrate Census (36 substrates under one Q0_64 scalar)
        Maps: every substrate → state/metric/transition/invariant/guard/scalar

7. Repository Structure

Path	Purpose
`0-Core-Formalism/lean/Semantics/`	Lean 4 source (truth), FixedPoint, PIST, GWL, AVMR, FAMM, etc.
`0-Core-Formalism/otom/`	One-Truth-Only-Model consolidated spec
`0-Core-Formalism/core/`	Rust/Python extraction targets
`1-Distributed-Systems/`	ENE mesh nodes, gossip, waveprobe
`2-Search-Space/manifold/`	Manifold compression algos (pist_gcl_compression.py, shifters/)
`3-Mathematical-Models/`	Equation registry, math databases, model maps
`4-Infrastructure/`	Shims, GPU, FPGA Verilog, drivers
`5-Applications/`	Scripts, tests, Hutter prize work, audit tools
`6-Documentation/docs/`	Main documentation tree
`docs/`	Research papers, specs, roadmaps (aliased into 6-Documentation)
`shared-data/`	Databases, golden traces, artifacts
`workspace-config/`	IDE and environment settings
`scratch/`	Experimental code

8. Settlements & Promotion Ladder

Settlement states (every artifact lives in one):

SEED → FORMING → STABLE → CRYSTALLIZED → COMPRESSED

Progression requires receipt-bearing evidence at each transition.

Promotion ladder (for models, not artifacts):

RAW_IDEA
  → SANITIZED_METAPHOR
  → TOY_MODEL
  → TYPED_MODEL
  → RESIDUAL_TESTED
  → COST_ACCOUNTED
  → PROOF_CANDIDATE
  → CORE_MODULE

Demotion is equally important — a broken proof goes back to COST_ACCOUNTED. A misleading analogy goes to METAPHOR_ONLY / ARCHIVED.

9. The Bounded Lawful Surface

Raw GCCL may be extremely expressive. Lawful GCCL is receipt-bounded.

A transition enters the lawful surface only if it satisfies:

valid syntax
+ declared projection
+ round-trip or explicit loss policy
+ invariant preservation
+ residual bound
+ KOT/cost bound
+ receipt
+ scale validity

No receipt, no promotion. No residual, no lawfulness claim.

10. Further Reading

6-Documentation/docs/AGENTS.md — Strict LLM operating rules (the constitution)
6-Documentation/docs/VISION_NORTH_STAR.md — Philosophical compass
6-Documentation/docs/GLOSSARY.md — Project-wide terminology
CONCEPTS.md — Quick reference for core concepts
6-Documentation/docs/roadmaps/ROADMAP.md — Master implementation timeline
6-Documentation/docs/research/FRAMEWORK_RELATIONSHIPS.md — GCCL/MISC/GENSIS layering
GETTING_STARTED.md — Practical setup guide

Sovereign Research Stack — Architecture v1.0 (2026-05-04)

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