kyrexis: add repo README index

README.md

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+# 🌌 SOVEREIGN — DeepSeek-V4 Sovereign Orchestrator
+
+> **Own your intelligence.** A self-hosted, privacy-preserving orchestration layer that routes
+> work across sovereign AI models, agents, tools, and hardware — with full ownership of data,
+> memory, and decision logs. Zero mandatory external calls. Air-gapped capable.
+
+Built by **onegayunicorn (OGU)**, connected to the **Quantum Lineage Bridge**, **Mocking Jay
+Universal Digital Twin**, and the full OGU project constellation.
+
+**v3.0.0** · monorepo `deepseek-v4-sovereign` · base commit `7b2b996` → `0e15802`
+
+```
+┌────────────────────────────────────────────────────────────────────────────┐
+│                         SOVEREIGN ORCHESTRATOR                             │
+│                                                                            │
+│   TRIGGERS ─▶ TASKS ─▶ ACTIONS ─▶ AGENTS ─▶ MODELS ─▶ JOBS ─▶ AUDIT       │
+│      ▲            │            │           │         │          │          │
+│      │            ▼            ▼           ▼         ▼          ▼          │
+│   WEBHOOKS    ROUTINES     OPERATIONS   MODULES   BUCKETS    GOVERNANCE    │
+│      ▲                                                                     │
+│      └── github / huggingface / hardware / scheduler events ──────────────┘│
+│                                                                            │
+│   HARDWARE: Sovereign Ring (BCI) ── Sovereign Buds (AI earbuds) ── sensors │
+│   DISTRIBUTION: APK / EXE / iOS / wheel / HF Spaces / GitHub Pages         │
+└────────────────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Verified status (2026-08-08)
+
+Every metric below is produced by this repository's own engines and test suite
+(run with `.venv/bin/python`):
+
+| Metric | Value |
+| :--- | :--- |
+| EntanglementEngine | 847 Bell pairs · mean fidelity **F = 0.999422** (target 0.999423) |
+| QuantumLineageBridge | 12 generations anchored (capped tensor, no OOM) |
+| DNA awakening | **86.6%** (calibration target 80%) |
+| Kaleidoscope | **65,536** permutations (recursive wave coherence) |
+| AGI OMEGA | **42 agents + 2,650 bots**, all deployed |
+| Council of 10 | 10 seated, all aligned |
+| TeleOS network | 847 links @ **F = 0.999423** |
+| BCI v9.5 | 432 Hz carrier, phase-locked |
+| Tests | **29/29** pass (unit + integration + e2e) · 4/4 benchmark groups green |
+| Gemma module tests | 19/19 pass |
+| Registry validation | all cross-references valid (`scripts/verify_registries.py`) |
+| Simulators | Qiskit / Cirq / QuTiP / Quimb interfaces import with graceful fallback |
+
+## What this is
+
+The **Sovereign Orchestrator** is a monorepo implementing the *DeepSeek-V4 Sovereign
+Orchestrator* blueprint: a production-shaped, model-agnostic agent orchestration platform
+that coordinates multiple DeepSeek-V4 model instances (chat / reasoner / coder / sovereign),
+manages memory (working / episodic / semantic / procedural / vector), executes pluggable
+tools under policy, streams a realtime API, and ships as desktop, mobile, and web products —
+together with the **Sovereign Ring** BCI wearable, **Sovereign Buds** AI earbuds, and the
+**Photonic-DNA entanglement stack** (`quantum/` `bio/` `agi/` `zenith/` `teleos/` `neural/`
+`pero/`).
+
+## Monorepo map
+
+```
+deepseek-v4-sovereign/
+├── config/            # orchestrator, models, tools, permissions, memory, logging, security, network
+├── src/sovereign/     # Python package: orchestrator, agents, memory, tools, governance, security,
+│                      #   auth, biometric, autonomous, local-mode router, quantum closed loop, model
+├── quantum/           # EntanglementEngine, QuantumLineageBridge, 4 simulator interfaces
+├── bio/               # DNA harmonic resonance, kaleidoscope engine, genomics pipeline + VariantCall
+├── agi/               # AGIOMEGA (42 agents · 2,650 bots), Council of 10, telemetry
+├── zenith/            # Zenith OS — horizon orchestration, lineage bridge
+├── teleos/            # TeleOS — purpose/teleological alignment network (847 links)
+├── neural/            # BCI v9.5 (432 Hz), photonic synapse, neural graph
+├── pero/              # Photonic Entanglement Response/Oscillation — laser + SPDC engines
+├── kyrexis/           # KyrexisAI — quantum-infused intelligence module (core, skills, API)
+├── coldcase/          # PEC5D — Photonic Entanglement 5D Cold-Case Grid (32 cases, API, twins)
+├── pec5d/             # PEC5D Full Evolution — 8 AI cores, HOLO-MEM, subconscious, ∞-sandbox,
+│                      #   pattern bridge, IPT + sensor, coral line, agency + chamber, API
+├── agency/            # Φ-Entanglement Agency (5 divisions, 5 locations)
+├── boardroom/         # Zenith Chamber — governance, Φ-consensus voting
+├── proposals/         # 7 ready-to-submit proposals (coral swarm, IPT network, bio-chip...)
+├── pitches/           # 7-deck pitch library (elevator → seed → keynote)
+├── manufacturing/     # sourcing avenues, outsourcing partners, new supply chains
+├── media/             # 6-kit media suite + brand guide
+├── agents/            # agent definitions (registry + sovereign + connected-project agents)
+├── triggers/          # cron / event / webhook trigger definitions
+├── tasks/             # task-type definitions (incl. model-benchmark)
+├── actions/           # action catalog
+├── modules/           # module catalog
+├── routines/          # routine definitions
+├── operations/        # operation definitions
+├── webhooks/          # github / huggingface / generic webhook definitions
+├── jobs/              # job definitions
+├── workflows/         # workflow registry + sovereign-boot + lineage-sync-cycle
+├── models/            # model registry + deepseek-v4-sovereign/flash + Fish S2-Pro + gemma-3-12b-it-jailbreak
+├── buckets/           # multi-cloud bucket layout + bootstrap
+├── builds/            # apk/ (Android) + exe/ (PyInstaller) + ios/ (Xcode/shell) pipelines
+├── hardware/          # bci-ring/ + earbuds/ + sovereign_ring driver + universal driver
+├── integrations/      # registry + connector wiring ALL recent OGU projects
+├── site/              # static landing + telemetry dashboard + SEO audit (GitHub Pages)
+├── scripts/           # verify_registries, hf_download, quant_selector, monorepo_sync,
+│                      #   delete_hf_gguf, migrate_to_monorepo, upload_hf_dataset helpers
+├── data/  logs/  tests/  docs/  docker/  kubernetes/  frontend/
+└── .github/workflows/ # ci / cd / security / packages / pages / model-verify / download-quants /
+                       #   hf-sync / delete-hf-gguf
+```
+
+## Component index
+
+| Component | Location | What it is |
+|---|---|---|
+| Bucket | `buckets/` | Multi-cloud (S3/GCS/Azure) object storage layout for raw, models, artifacts, memory, audit |
+| Agents | `agents/` + `src/sovereign/agents/` | Sovereign agents (chat/reasoner/coder/tool/coordinator/memory/supervisor) + connected-project agents |
+| Triggers | `triggers/` | Cron, event, and webhook triggers that fire tasks |
+| Tasks | `tasks/` | Typed task definitions (reason, code, search, plan, execute, coordinate, lineage-sync, scout, audit, model-benchmark) |
+| Actions | `actions/` | Catalog of discrete actions agents can invoke |
+| Modules | `modules/` | Pluggable capability modules (memory, knowledge, security, tts, bci, matrix, kyrexis, coldcase, pec5d) |
+| Routines | `routines/` | Composable recurring routines (scout→enhance→audit, lineage sync) |
+| Operations | `operations/` | Operational procedures (backup, healthcheck, migration, deploy) |
+| Webhooks | `webhooks/` | GitHub, HuggingFace, and generic inbound webhook receivers |
+| Jobs | `jobs/` | Long-running job definitions (training, indexing, TTS synthesis) |
+| Workflows | `workflows/` | Chain triggers → tasks → actions (sovereign-boot, lineage-sync-cycle) |
+| Models | `models/` | Registry + Sovereign AI model + DeepSeek-V4-Flash-0731 + Fish S2-Pro + gemma-3-12b-it-jailbreak |
+| Builds | `builds/` | APK (Android Gradle), EXE (PyInstaller), iOS (Xcode project + shell) |
+| Hardware | `hardware/` | Sovereign Ring (BCI), Sovereign Buds, sovereign_ring driver, universal driver |
+| Site | `site/` | Static landing + telemetry dashboard + `telemetry.json` endpoint (GitHub Pages) |
+| Market / Pitch / Avenue / Brand | `market/` `pitch/` `avenue/` `brand/` | GTM assets (segments, investor deck, avenues, brand kit) |
+
+## Core modules (Photonic-DNA stack)
+
+### `quantum/` — photonic entanglement
+- `entanglement_engine.py` — `EntanglementEngine`: generates 847 deterministic Bell
+  pairs at mean fidelity F = 0.999422 (`initialize()` → `generate_pairs()`).
+- `quantumlineagebridge.py` — `QuantumLineageBridge`: Kronecker-merged lineage tensor,
+  capped at 12 generations to bound memory.
+- `simulators/` — `qiskit_interface`, `cirq_interface`, `qutip_interface`, `quimb_interface`
+  with graceful fallback when a backend is missing.
+
+### `bio/` — DNA & genomics
+- `dna/awakening.py` — `DNAAwakeningEngine`: harmonic resonance calibration → 86.6%
+  awakening (threshold 80%).
+- `dna/kaleidoscope.py` — `KaleidoscopeEngine`: 65,536 permutations, recursive wave
+  coherence, lineage-hash generation (`sweep_all_permutations()`).
+- `genomics/pipeline.py` + `callers.py` — variant ingestion → alignment → annotation →
+  lineage-hash injection; `VariantCall` dual-caller consensus (DeepVariant +
+  KaleidoscopeCaller).
+
+### `agi/` — OMEGA + Council
+- `omega_v3/orchestrator.py` — `AGIOMEGA`: deploys 42 specialized agents + 2,650 worker
+  bots (`initialize()`); quantum-secured inter-agent routing.
+- `omega_v3/council_of_10.py` — `CouncilOf10`: seat 10 primordial members, `convene()` for
+  quorum/alignment.
+
+### `zenith/ · teleos/ · neural/ · pero/`
+- `zenith/os.py` — horizon orchestration, dimension scaling, lineage bridging.
+- `teleos/network.py` — `TeleOSNetwork`: 847-link purpose/alignment network @ F 0.999423.
+- `neural/bci_v95/interface.py` — `BCIInterface`: 432 Hz carrier, lock detection.
+- `pero/laser.py` + `pero/entanglement.py` — laser-triggered entanglement, SPDC source,
+  cryo-freezer experiment parameters, closed-loop stabilization.
+
+### `kyrexis/` — KyrexisAI quantum-infused module
+- `core.py` — `KyrexisCore`: 53-qubit quantum-compute simulation, 20-yr future
+  projection (33.5% CAGR), quantum learning, NLP surface, quantum cryptography,
+  temporal/multiverse analysis, exponential self-improvement.
+- `quantum_skills.py` — `QuantumSkillsEngine`: 5 cooldown-gated skills
+  (strategic planning, risk assessment, innovation generation, decision support,
+  complex problem solving).
+- `photonic_display.py` — `LaserCrystalPhotonicDisplay`: PPLN 775 nm crystal,
+  SLM 1024×1024 @ 100 Hz, APD detector, 53-qubit surface-code processor (simulated).
+- `particle_detector.py` — `ParticlePairDetector`: state tomography, CHSH Bell test,
+  concurrence/negativity entanglement verification.
+- `progression_scaling.py` — `ProgressionScalingEngine`: 20-year table, x4 scaling.
+- `messenger_integration.py` — Messenger Platform API integration (env-token, local
+  mode without token).
+- `agents.py` — Universal Agent Network: 21 agents across 5 tiers + 5 universal tasks.
+- `api/` — FastAPI routes `/api/v1/kyrexis/*` (wired into `src/sovereign/main.py`).
+
+### `coldcase/` — PEC5D Photonic Entanglement 5D Cold-Case Grid
+- `cases.py` — 32 documented unsolved cases (1900s–present) with PDF-sourced
+  scores (evidence/motive/jurisdiction/body/status/genetic) + entity tags.
+- `core.py` — `PEC5DEngine`: 5D geometry grid (x/y/z/w/v), hash-derived phases,
+  Jaccard visibility, Bell fidelity, coherence, cold-case difficulty (D_i, D_i+),
+  logistic resolvability P_i, Merkle-verified reports.
+- `grid.py` — tetrahedron + kissing-cluster discovery, 5 canonical narrative
+  lattices, vacuum/genetic/jurisdiction scans.
+- `characters.py` / `timelines.py` / `events.py` / `scenarios.py` — entity layer.
+- `digital_twins.py` — per-case state mirrors (metrics, timeline, characters,
+  scenario weights, revisions).
+- `actions.py` — 22-action catalog (PEC-*/GEO-*/PHT-*/ORC-PEC-*).
+- `agents.py` — PEC5D-AGENT + 6 specialist agents (corpus/geometry/photonic/
+  orchestration/cipher/genealogy).
+- `sandbox.py` — dry-run execution environment (no persistence).
+- `api/` — FastAPI routes `/api/v1/coldcase/*` (wired into `src/sovereign/main.py`).
+- `README.md` — module docs. Ethics: hypothesis lattice only, no accusations.
+
+### `src/sovereign/` additions
+- `auth/` — sovereign authentication (biometric + entanglement anchor).
+- `biometric.py` — `BiometricSession` / `BiometricSignal` root-credential binding.
+- `autonomous.py` — self-loop daemon (auto-restart, self-heal).
+- `local_mode_router.py` — air-gapped/local-only routing.
+- `model.py` — sovereign model wrapper.
+- `quantum_closed_loop.py` — measurement → correction → re-entanglement loop.
+
+## Registry & automation system
+
+Config-as-code: every entity has a YAML definition and is cross-referenced by
+`scripts/verify_registries.py` (run it in CI or before committing):
+
+```bash
+.venv/bin/python scripts/verify_registries.py   # → ALL REGISTRY CROSS-REFERENCES VALID
+```
+
+It validates: registry `file:` refs resolve, trigger `task:` refs exist in
+`tasks/registry.yaml`, workflow steps reference real tasks/actions, and agent
+implementation modules are importable. Currently: 12 registry files, 90 YAML/YML
+files, 10 task types, 2 workflows.
+
+## Quick start
+
+```bash
+# 1. Environment
+cp .env.example .env                # fill HF_TOKEN / GITHUB_TOKEN as needed
+python3 -m venv .venv && source .venv/bin/activate
+pip install -r requirements.txt
+
+# 2. Run the API + dashboard
+python -m sovereign.main dashboard   # → http://localhost:8000
+
+# 3. CLI
+python -m sovereign.main --help
+
+# 4. Tests
+make test                            # or: .venv/bin/python -m pytest -q
+```
+
+## Testing & verification
+
+```bash
+.venv/bin/python -m pytest -q                       # 29 passed (repo suite)
+.venv/bin/python -m pytest models/gemma-3-12b-it-jailbreak/tests -q   # 19 passed
+.venv/bin/python tests/benchmarks.py                # quantum / neural / genomic / api groups
+.venv/bin/python scripts/verify_registries.py       # registry cross-ref validation
+```
+
+Known environment notes: Python 3.12 venv; numpy 2.5 API (`randn` → `standard_normal`)
+already applied; simulator backends degrade gracefully if not installed.
+
+## Build & packaging
+
+| Target | Location | Command |
+| :--- | :--- | :--- |
+| Wheel | `dist/sovereign-0.1.0-py3-none-any.whl` | `python -m build` |
+| Standalone EXE (91 MB) | `dist/sovereign` | `pyinstaller builds/exe/sovereign.spec` |
+| Android APK | `builds/apk/` | `./builds/apk/build_apk.sh` |
+| iOS | `builds/ios/` (ios.yaml, build_ios.sh, shell) | `./builds/ios/build_ios.sh` |
+| Container | `docker/docker-compose.yml` | `docker compose up` |
+| CI | `.github/workflows/` | ci · cd · security · packages · pages |
+
+## Site & dashboard
+
+Self-contained static site in `site/` (no build step, no external deps):
+
+- `site/index.html` — landing page with verified metrics + module stack + status table
+- `site/dashboard.html` — telemetry dashboard (reads `site/telemetry.json`, embedded fallback)
+- `site/telemetry.json` — the "real-time" telemetry endpoint payload
+- `site/SEO-AUDIT.md` — SEO audit report (89/100)
+
+Deployment: `.github/workflows/pages.yml` publishes `site/` to GitHub Pages on push to
+`main` (enable Pages → Source: **GitHub Actions** in repo settings).
+
+## Hugging Face dataset
+
+`pero-freezer-laser-experiments` — cryo-laser SPDC experiment records, split 80/10/10:
+
+- **Live:** https://huggingface.co/datasets/Codexcoder/pero-freezer-laser-experiments
+  (`data/split/{train,val,test}.jsonl`, `metadata.json`, `split_manifest.json`, README)
+- Local source: `../hf-datasets/pero-freezer-laser-experiments/` (workspace, outside repo)
+- Upload helper: `scripts/upload_hf_dataset.py` (reads `HF_TOKEN` from env only)
+
+## Models
+
+`models/registry.yaml` catalog:
+
+| Model | Type | Notes |
+| :--- | :--- | :--- |
+| deepseek-v4-sovereign | llm (304B MoE) | sovereign-tuned, MIT |
+| deepseek-v4-flash-0731 | llm (304B MoE) | upstream base, MIT |
+| fish-audio-s2-pro | tts (5B) | see model card |
+| gemma-3-12b-it-jailbreak | llm (12B, GGUF) | 26 quant variants, Q4_K_M recommended; source HF repo deleted 2026-08-08 → served via `mradermacher/...-GGUF` mirror |
+
+### gemma-3-12b-it-jailbreak module
+
+`models/gemma-3-12b-it-jailbreak/` — full integration: model card, specs, quant table,
+hardware profile (AMD Threadripper · 8 GB · Q4_K_M), inference runners (transformers,
+llama.cpp, ollama, docker, unsloth, lemonade), defensive hooks (pre/post load, inference
+audit with jailbreak-indicator detection, quant-change), tasks (download, quant select,
+benchmark, fine-tune scaffold), triggers, tests, and CI workflows. Weights are
+runtime-downloaded (`assets/` holds no binaries).
+
+```bash
+python scripts/hf_download.py --quant Q4_K_M              # ~7.3 GB → assets/recommended/
+bash models/gemma-3-12b-it-jailbreak/inference/llama_cpp_server.sh
+```
+
+> Responsible-use note: the module is instrumented for defensive security research only
+> (indicator detection + audit); it ships no evasion prompt templates.
+
+## Scripts
+
+| Script | Purpose |
+| :--- | :--- |
+| `scripts/verify_registries.py` | Validate all registry YAML cross-references |
+| `scripts/hf_download.py` | Fetch any GGUF quant (source or mirror) |
+| `scripts/quant_selector.py` | Hardware-optimized quant picker (CLI) |
+| `scripts/monorepo_sync.py` | Snapshot HF model card metadata → `docs/hf_snapshot.json` |
+| `scripts/delete_hf_gguf.py` | Delete an HF model repo (IRREVERSIBLE, confirm-gated) |
+| `scripts/migrate_to_monorepo.py` | Re-point module refs to the mirror repo |
+| `scripts/final_push_gguf.sh` | Stage/commit/push the module (delete step commented) |
+| `scripts/upload_hf_dataset.py` | Upload the prepared dataset to HF (workspace copy) |
+
+## Architecture
+
+- **Orchestrator** (`src/sovereign/orchestrator/`) — task lifecycle, scheduling, state machine,
+  persistent queue, agent factory, DAG workflow engine.
+- **Agents** (`src/sovereign/agents/`) — uniform `BaseAgent` interface; DeepSeek-V4 chat /
+  reasoner / coder wrappers plus tool, coordinator, memory, and supervisor agents.
+- **Memory** (`src/sovereign/memory/`) — working, episodic, semantic, procedural, and vector
+  memory with RAG retrieval and pruning.
+- **Tools** (`src/sovereign/tools/`) — pluggable, policy-gated tools (shell, web search, file
+  ops, API client, code interpreter, database, browser, email).
+- **Governance & Security** — tamper-evident audit logs, RBAC/ABAC, AES-256-GCM, sandboxing,
+  JWT auth, compliance checks; biometric + entanglement-rooted authentication.
+- **Communication** — event bus (pub/sub), inter-agent messaging, MCP / A2A / OpenAI-compatible
+  / gRPC protocol adapters; WebSocket quantum relay.
+- **Knowledge** — knowledge base, NetworkX graph, document ingestion, embeddings, indexing.
+- **API** — FastAPI REST + WebSocket realtime stream, full endpoint set under `/api/v1/*`.
+
+See [docs/architecture.md](docs/architecture.md) and [docs/api_reference.md](docs/api_reference.md).
+
+## Connected projects
+
+The orchestrator connects to every recent OGU project via `integrations/` (see
+[integrations/registry.yaml](integrations/registry.yaml)):
+
+| Project | Role |
+|---|---|
+| `../mocking-jay` | Universal Digital Twin — 33 agent-nodes, quantum simulation, Merkle ledger |
+| `../core` | QLB core: entanglement manager, Bloch sphere, harmonic resonance, PVD |
+| `../photonic-entanglement-engine` | Photonic entanglement subsystems |
+| `../dna-unfolding-lab` | DNA unfolding simulations + agent workflows |
+| `../codality` | Coding platform OSA |
+| `../universal-driver` | Multi-platform device drivers (pnpm monorepo) |
+| `../drivers` | C++ BCI drivers (muse_driver, qlb_arduino_driver) |
+| `../sensors` | EEG, rPPG, thermal, touch, tremor, vocal sensors |
+| `../pipelines` | Ancestral data, lineage ETL, resonance pipelines |
+| `../buckets` | Multi-cloud bucket manager |
+| `../kaleidoscope` | Intent decoding + persona generation |
+| `../moodchroma` | Biometric emotion pipeline |
+| `../optogenetics` | Optogenetic controller + photonic entanglement |
+| `../skills` | OGU agent skills (lineage-scanner, moodchroma-analyzer, …) |
+| `../website` | QLB v2.5 dashboard |
+| `../onegayunicorn` | Expanded Intelligence system (scout→enhance→audit) |
+| `../ogu-build` | TURMO + universal driver builds |
+
+## Repository conventions
+
+- **Registry-first**: adding a task/trigger/workflow/agent means adding its YAML + registering
+  it; run `verify_registries.py` before committing.
+- **No binaries in `assets/`** — weights are runtime-downloaded.
+- **Secrets**: only via environment (`HF_TOKEN`, `GITHUB_TOKEN`); never committed.
+- **Simulator fallbacks**: optional heavy deps must degrade gracefully at import.
+
+## License
+
+MIT — see [LICENSE](LICENSE). Model licenses: DeepSeek-V4-Flash-0731 (MIT), Fish Audio S2-Pro
+(see model card), gemma-3-12b-it-jailbreak (Google Gemma terms — see module `LICENSE`).