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.*

index.html

@@ -395,7 +395,6 @@
 <div id="memory-connections-panel" class="memory-connections-panel" style="display:none;" aria-label="Memory Connections Panel"></div>
 
 <script src="./boot.js"></script>
-<script src="./js/heartbeat.js"></script>
 <script src="./avatar-customization.js"></script>
 <script src="./lod-system.js"></script>
 <script>

js/heartbeat.js

@@ -1,293 +0,0 @@
-/**
- * WebSocket Heartbeat Client for The Nexus
- * Issue #1535: feat: WebSocket heartbeat with auto-reconnect from client
- * 
- * Provides:
- * - Client sends heartbeat ping every 30s
- * - Server responds with pong + user count
- * - Client auto-reconnects on missed 2 heartbeats
- * - Reconnect preserves user position/identity
- */
-
-class NexusHeartbeat {
-    constructor(options = {}) {
-        this.heartbeatInterval = options.heartbeatInterval || 30000; // 30 seconds
-        this.maxMissedHeartbeats = options.maxMissedHeartbeats || 2;
-        this.reconnectDelay = options.reconnectDelay || 1000; // 1 second
-        this.maxReconnectDelay = options.maxReconnectDelay || 30000; // 30 seconds
-        
-        this.ws = null;
-        this.heartbeatTimer = null;
-        this.missedHeartbeats = 0;
-        this.isConnected = false;
-        this.userId = options.userId || this.generateUserId();
-        this.position = options.position || { x: 0, y: 0, z: 0 };
-        this.reconnectAttempts = 0;
-        
-        // Callbacks
-        this.onConnect = options.onConnect || (() => {});
-        this.onDisconnect = options.onDisconnect || (() => {});
-        this.onHeartbeat = options.onHeartbeat || (() => {});
-        this.onUserCount = options.onUserCount || (() => {});
-        this.onError = options.onError || console.error;
-        
-        // Bind methods
-        this.connect = this.connect.bind(this);
-        this.disconnect = this.disconnect.bind(this);
-        this.sendHeartbeat = this.sendHeartbeat.bind(this);
-        this.handleMessage = this.handleMessage.bind(this);
-        this.handleClose = this.handleClose.bind(this);
-        this.handleError = this.handleError.bind(this);
-    }
-    
-    generateUserId() {
-        return 'user_' + Math.random().toString(36).substr(2, 9);
-    }
-    
-    connect(url) {
-        if (this.ws && this.ws.readyState === WebSocket.OPEN) {
-            console.warn('Already connected');
-            return;
-        }
-        
-        this.url = url;
-        console.log(`Connecting to ${url}...`);
-        
-        try {
-            this.ws = new WebSocket(url);
-            this.ws.onopen = this.handleOpen.bind(this);
-            this.ws.onmessage = this.handleMessage;
-            this.ws.onclose = this.handleClose;
-            this.ws.onerror = this.handleError;
-        } catch (error) {
-            this.onError('Failed to create WebSocket:', error);
-            this.scheduleReconnect();
-        }
-    }
-    
-    disconnect() {
-        console.log('Disconnecting...');
-        
-        // Stop heartbeat
-        this.stopHeartbeat();
-        
-        // Close WebSocket
-        if (this.ws) {
-            this.ws.onclose = null; // Prevent reconnect on manual disconnect
-            this.ws.close(1000, 'Manual disconnect');
-            this.ws = null;
-        }
-        
-        this.isConnected = false;
-        this.missedHeartbeats = 0;
-        this.reconnectAttempts = 0;
-    }
-    
-    handleOpen() {
-        console.log('Connected to WebSocket');
-        this.isConnected = true;
-        this.missedHeartbeats = 0;
-        this.reconnectAttempts = 0;
-        
-        // Send reconnect message with user info
-        this.sendReconnect();
-        
-        // Start heartbeat
-        this.startHeartbeat();
-        
-        // Call connect callback
-        this.onConnect();
-    }
-    
-    handleMessage(event) {
-        try {
-            const data = JSON.parse(event.data);
-            
-            if (data.type === 'pong') {
-                // Reset missed heartbeats
-                this.missedHeartbeats = 0;
-                
-                // Update user count
-                if (data.user_count !== undefined) {
-                    this.onUserCount(data.user_count);
-                }
-                
-                // Call heartbeat callback
-                this.onHeartbeat(data);
-                
-                console.debug('Heartbeat pong received');
-            } else if (data.type === 'health') {
-                // Health check response
-                console.debug('Health check:', data);
-            } else {
-                // Regular message
-                console.debug('Message received:', data);
-            }
-        } catch (error) {
-            // Not JSON or parse error
-            console.debug('Non-JSON message received:', event.data);
-        }
-    }
-    
-    handleClose(event) {
-        console.log(`WebSocket closed: ${event.code} ${event.reason}`);
-        this.isConnected = false;
-        this.stopHeartbeat();
-        
-        // Call disconnect callback
-        this.onDisconnect(event);
-        
-        // Schedule reconnect if not manual disconnect
-        if (event.code !== 1000) {
-            this.scheduleReconnect();
-        }
-    }
-    
-    handleError(error) {
-        this.onError('WebSocket error:', error);
-    }
-    
-    startHeartbeat() {
-        if (this.heartbeatTimer) {
-            clearInterval(this.heartbeatTimer);
-        }
-        
-        console.log(`Starting heartbeat every ${this.heartbeatInterval / 1000}s`);
-        
-        this.heartbeatTimer = setInterval(() => {
-            this.sendHeartbeat();
-        }, this.heartbeatInterval);
-        
-        // Send initial heartbeat
-        this.sendHeartbeat();
-    }
-    
-    stopHeartbeat() {
-        if (this.heartbeatTimer) {
-            clearInterval(this.heartbeatTimer);
-            this.heartbeatTimer = null;
-        }
-    }
-    
-    sendHeartbeat() {
-        if (!this.isConnected || !this.ws || this.ws.readyState !== WebSocket.OPEN) {
-            console.warn('Cannot send heartbeat: not connected');
-            return;
-        }
-        
-        const heartbeat = {
-            type: 'heartbeat',
-            timestamp: Date.now(),
-            user_id: this.userId,
-            position: this.position
-        };
-        
-        try {
-            this.ws.send(JSON.stringify(heartbeat));
-            console.debug('Heartbeat sent');
-            
-            // Check for missed heartbeats
-            this.missedHeartbeats++;
-            if (this.missedHeartbeats > this.maxMissedHeartbeats) {
-                console.warn(`Missed ${this.missedHeartbeats} heartbeats, reconnecting...`);
-                this.ws.close(4000, 'Missed heartbeats');
-            }
-        } catch (error) {
-            this.onError('Failed to send heartbeat:', error);
-            this.ws.close(4001, 'Heartbeat send failed');
-        }
-    }
-    
-    sendReconnect() {
-        if (!this.isConnected || !this.ws || this.ws.readyState !== WebSocket.OPEN) {
-            console.warn('Cannot send reconnect: not connected');
-            return;
-        }
-        
-        const reconnect = {
-            type: 'reconnect',
-            timestamp: Date.now(),
-            user_id: this.userId,
-            position: this.position
-        };
-        
-        try {
-            this.ws.send(JSON.stringify(reconnect));
-            console.log('Reconnect message sent');
-        } catch (error) {
-            this.onError('Failed to send reconnect:', error);
-        }
-    }
-    
-    scheduleReconnect() {
-        if (this.reconnectAttempts >= 10) {
-            console.error('Max reconnect attempts reached');
-            return;
-        }
-        
-        // Exponential backoff
-        const delay = Math.min(
-            this.reconnectDelay * Math.pow(2, this.reconnectAttempts),
-            this.maxReconnectDelay
-        );
-        
-        console.log(`Reconnecting in ${delay / 1000}s (attempt ${this.reconnectAttempts + 1})...`);
-        
-        setTimeout(() => {
-            this.reconnectAttempts++;
-            this.connect(this.url);
-        }, delay);
-    }
-    
-    updatePosition(x, y, z) {
-        this.position = { x, y, z };
-        
-        // Send position update if connected
-        if (this.isConnected && this.ws && this.ws.readyState === WebSocket.OPEN) {
-            const update = {
-                type: 'position',
-                timestamp: Date.now(),
-                user_id: this.userId,
-                position: this.position
-            };
-            
-            try {
-                this.ws.send(JSON.stringify(update));
-            } catch (error) {
-                console.warn('Failed to send position update:', error);
-            }
-        }
-    }
-    
-    getUserId() {
-        return this.userId;
-    }
-    
-    getPosition() {
-        return { ...this.position };
-    }
-    
-    isConnectionActive() {
-        return this.isConnected && this.ws && this.ws.readyState === WebSocket.OPEN;
-    }
-    
-    getStats() {
-        return {
-            connected: this.isConnected,
-            userId: this.userId,
-            position: this.position,
-            missedHeartbeats: this.missedHeartbeats,
-            reconnectAttempts: this.reconnectAttempts
-        };
-    }
-}
-
-// Export for use in other modules
-if (typeof module !== 'undefined' && module.exports) {
-    module.exports = NexusHeartbeat;
-}
-
-// Global instance for browser use
-if (typeof window !== 'undefined') {
-    window.NexusHeartbeat = NexusHeartbeat;
-}