Merge branch 'main' into fix/1644

Restores the missing GENOME.md file which provides a comprehensive
map of the Nexus codebase for developers and AI agents.

## Contents
- Overview and key stats
- Architecture diagram
- Frontend systems (3D world, GOFAI, memory, audio)
- Backend services (WebSocket, scripts, tools)
- Data files and configuration
- Testing instructions
- Key patterns (component, WebSocket, portal schema)
- Security summary
- Related repos
- Quick start guide

Closes #1644

GENOME.md

@@ -0,0 +1,234 @@
+# GENOME.md — The Nexus Codebase Architecture Map
+
+**Generated**: 2026-04-20
+**Repository**: Timmy_Foundation/the-nexus
+**Purpose**: Comprehensive map of the Nexus codebase for developers and AI agents.
+
+---
+
+## Overview
+
+The Nexus is Timmy's canonical 3D/world repository — a sovereign AI agent visualization surface and local-first training ground. It combines a Three.js 3D browser world with Python cognition components, WebSocket bridges, and fleet orchestration tools.
+
+**Key Stats**:
+- ~357 source files
+- 201 Python files
+- 23 JavaScript files
+- 107 Markdown docs
+- 24 Shell scripts
+
+---
+
+## Architecture
+
+```
+the-nexus/
+├── app.js                    # Main Three.js 3D world (frontend entry)
+├── index.html                # HTML shell
+├── style.css                 # Global styles
+├── server.py                 # WebSocket gateway
+├── gofai_worker.js           # GOFAI web worker
+├── portals.json              # Portal registry
+├── vision.json               # Vision points config
+├── provenance.json           # File integrity hashes
+│
+├── nexus/                    # Python cognition layer
+│   ├── components/           # Frontend JS modules
+│   ├── mnemosyne/            # Memory system
+│   ├── mempalace/            # Long-term memory
+│   └── symbolic-engine.js    # GOFAI rules
+│
+├── scripts/                  # Operational scripts
+├── bin/                      # CLI tools
+├── tests/                    # Test suite
+├── docs/                     # Documentation
+└── config/                   # Configuration files
+```
+
+---
+
+## Frontend (Browser World)
+
+### Entry Points
+| File | Purpose |
+|------|---------|
+| `index.html` | HTML shell, HUD layout |
+| `app.js` | Main Three.js app (~141K lines) |
+| `style.css` | All styles (~61K) |
+| `gofai_worker.js` | Off-thread GOFAI reasoning |
+
+### Core Systems
+| System | File | Description |
+|--------|------|-------------|
+| 3D World | `app.js` | Three.js scene, camera, rendering |
+| GOFAI | `app.js` | Symbolic rules, blackboard, planner |
+| Memory | `nexus/components/spatial-memory.js` | 3D memory crystals |
+| Audio | `nexus/components/spatial-audio.js` | Spatial sound system |
+| Portals | `portals.json` | External service links |
+| Chat | `app.js` | Chat panel and messaging |
+| HUD | `app.js` + `style.css` | Heads-up display |
+
+### Components (`nexus/components/`)
+| Component | Purpose |
+|-----------|---------|
+| `spatial-memory.js` | 3D memory crystal visualization |
+| `spatial-audio.js` | Spatial sound for memories |
+| `memory-birth.js` | Memory creation animation |
+| `memory-pulse.js` | BFS pulse wave on click |
+| `memory-inspect.js` | Memory detail panel |
+| `memory-connections.js` | Connection graph |
+| `memory-particles.js` | Particle effects |
+| `memory-optimizer.js` | Memory cleanup |
+| `session-rooms.js` | Evennia room snapshots |
+| `timeline-scrubber.js` | Time navigation |
+| `resonance-visualizer.js` | Pattern visualization |
+| `portal-health-check.js` | Portal status monitoring |
+| `spatial-chat.js` | 3D audio chat notifications |
+
+---
+
+## Backend (Python)
+
+### Core Services
+| File | Purpose |
+|------|---------|
+| `server.py` | WebSocket gateway for real-time comms |
+| `multi_user_bridge.py` | Multi-user MUD bridge |
+| `gitea_api/` | Gitea API helpers |
+
+### Scripts (`scripts/`)
+| Script | Purpose |
+|--------|---------|
+| `cleanup-duplicate-prs.sh` | Close duplicate PRs |
+| `check-existing-prs.sh` | Pre-flight PR check |
+| `pr_backlog_analyzer.py` | PR backlog analysis |
+| `audit_mempalace_privacy.py` | Privacy audit |
+| `provision-runner.sh` | Runner setup |
+| `runner_health_probe.sh` | Health monitoring |
+
+### Bin Tools (`bin/`)
+| Tool | Purpose |
+|------|---------|
+| `enforce_branch_protection.py` | Branch protection enforcement |
+| `check_duplicate_milestones.py` | Milestone cleanup |
+| `generate_provenance.py` | Provenance hash generation |
+
+---
+
+## Data Files
+
+| File | Format | Purpose |
+|------|--------|---------|
+| `portals.json` | JSON | Portal registry (8 portals) |
+| `vision.json` | JSON | Vision points |
+| `world_state.json` | JSON | World state snapshot |
+| `provenance.json` | JSON | File integrity hashes |
+| `manifest.json` | JSON | PWA manifest |
+
+---
+
+## Configuration
+
+| File | Purpose |
+|------|---------|
+| `.gitea/branch-protection/` | Branch protection rules |
+| `.github/workflows/` | CI/CD workflows |
+| `config/` | Runtime configuration |
+| `pytest.ini` | Test configuration |
+
+---
+
+## Testing
+
+| Directory | Coverage |
+|-----------|----------|
+| `tests/` | Unit and integration tests |
+| `tests/test_provenance.py` | File integrity tests |
+| `tests/test_spatial_search.js` | Spatial search tests |
+
+Run tests:
+```bash
+python3 -m pytest tests/ -v
+node --test tests/*.js
+```
+
+---
+
+## Key Patterns
+
+### Component Pattern
+```javascript
+const ComponentName = (() => {
+  let _state = null;
+  
+  function init(config) { ... }
+  function update(delta) { ... }
+  
+  return { init, update };
+})();
+
+export { ComponentName };
+```
+
+### WebSocket Pattern
+```python
+async def handler(websocket):
+    async for message in websocket:
+        # Process and broadcast
+        pass
+```
+
+### Portal Schema
+```json
+{
+  "id": "portal-id",
+  "name": "Display Name",
+  "portal_type": "game-world",
+  "destination": { "url": "...", "type": "harness" }
+}
+```
+
+---
+
+## Security
+
+- WebSocket gateway binds to `127.0.0.1` by default
+- Optional token authentication via `NEXUS_WS_TOKEN`
+- Rate limiting on connections and messages
+- Branch protection on `main`
+- Provenance hash verification
+
+See `SECURITY.md` for full details.
+
+---
+
+## Related Repos
+
+| Repo | Relationship |
+|------|--------------|
+| `timmy-config` | Configuration and fleet management |
+| `hermes-agent` | Agent runtime |
+| `timmy-home` | SOUL.md and core docs |
+| `the-door` | Crisis detection system |
+
+---
+
+## Quick Start
+
+```bash
+# Clone
+git clone https://forge.alexanderwhitestone.com/Timmy_Foundation/the-nexus.git
+
+# Run WebSocket gateway
+python3 server.py
+
+# Open browser world
+open index.html
+
+# Run tests
+python3 -m pytest tests/
+```
+
+---
+
+*This GENOME.md is auto-maintained. Update when adding major new systems.*