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.*

app.js

@@ -734,8 +734,6 @@ async function init() {
     const response = await fetch('./portals.json');
     const portalData = await response.json();
     createPortals(portalData);
-    // Initialize portal health checks (#1539)
-    if (window.PortalHealthCheck) window.PortalHealthCheck.init(portals);
   } catch (e) {
     console.error('Failed to load portals.json:', e);
     addChatMessage('error', 'Portal registry offline. Check logs.');
@@ -3574,9 +3572,7 @@ function gameLoop() {
     animateMemoryOrbs(delta);
   }
 
-    updatePortalTunnel(delta, elapsed);
-    // Update portal health visuals (#1539)
-    if (window.PortalHealthCheck) window.PortalHealthCheck.update(portals);
+  updatePortalTunnel(delta, elapsed);
 
   if (workshopScanMat) workshopScanMat.uniforms.uTime.value = clock.getElapsedTime();
   if (activePortal !== lastFocusedPortal) {

index.html

@@ -396,7 +396,6 @@
 
 <script src="./boot.js"></script>
 <script src="./avatar-customization.js"></script>
-<script src="./portal-health-check.js"></script>
 <script src="./lod-system.js"></script>
 <script>
 function openMemoryFilter() { renderFilterList(); document.getElementById('memory-filter').style.display = 'flex'; }

portal-health-check.js

@@ -1,168 +0,0 @@
-/**
- * Portal Health Check Module (#1539)
- *
- * Monitors portal status and updates visuals:
- * - Dims offline/blocked portals
- * - Shows "Offline" tooltip
- * - Auto-re-enables when status changes to online
- * - Runs check every 5 minutes
- */
-
-(function () {
-  'use strict';
-
-  const CHECK_INTERVAL = 5 * 60 * 1000; // 5 minutes
-  const DIM_OPACITY = 0.15;
-  const NORMAL_OPACITY = 1.0;
-  const FADE_SPEED = 0.02;
-
-  let portalHealthStates = {}; // portal_id -> { healthy, fading, currentOpacity, targetOpacity }
-  let checkTimer = null;
-
-  // ═══ Health Check ═══════════════════════════════════════════
-  function checkPortalHealth(portals, wsConnected) {
-    for (const portal of portals) {
-      const id = portal.config.id;
-      const status = portal.config.status || 'unknown';
-      const blocked = portal.config.blocked_reason;
-      const interactionReady = portal.config.interaction_ready !== false;
-
-      // Determine health
-      const healthy = status === 'online' && !blocked && interactionReady && wsConnected;
-
-      if (!portalHealthStates[id]) {
-        portalHealthStates[id] = { healthy: true, currentOpacity: NORMAL_OPACITY, targetOpacity: NORMAL_OPACITY };
-      }
-
-      const state = portalHealthStates[id];
-      const wasHealthy = state.healthy;
-      state.healthy = healthy;
-      state.targetOpacity = healthy ? NORMAL_OPACITY : DIM_OPACITY;
-
-      // Log state changes
-      if (wasHealthy !== healthy) {
-        const label = portal.config.name || id;
-        if (healthy) {
-          console.log(`[PortalHealth] ${label} — back online`);
-        } else {
-          const reason = blocked || (!wsConnected ? 'bridge offline' : `status: ${status}`);
-          console.log(`[PortalHealth] ${label} — offline (${reason})`);
-        }
-      }
-    }
-  }
-
-  // ═══ Visual Update ══════════════════════════════════════════
-  function updatePortalVisuals(portals) {
-    for (const portal of portals) {
-      const id = portal.config.id;
-      const state = portalHealthStates[id];
-      if (!state) continue;
-
-      // Smooth fade toward target opacity
-      if (Math.abs(state.currentOpacity - state.targetOpacity) > 0.01) {
-        state.currentOpacity += (state.targetOpacity - state.currentOpacity) * FADE_SPEED;
-      } else {
-        state.currentOpacity = state.targetOpacity;
-      }
-
-      const opacity = state.currentOpacity;
-      const dimmed = opacity < NORMAL_OPACITY * 0.5;
-
-      // Apply to portal meshes
-      if (portal.ring) {
-        portal.ring.material.opacity = opacity;
-        portal.ring.material.transparent = true;
-        portal.ring.material.emissiveIntensity = dimmed ? 0.2 : 1.5;
-      }
-
-      if (portal.swirl) {
-        portal.swirl.material.uniforms.uTime.value += dimmed ? 0.001 : 0.016; // Slow/stop swirl when offline
-        portal.swirl.material.opacity = opacity;
-      }
-
-      if (portal.pSystem) {
-        portal.pSystem.material.opacity = opacity * 0.6;
-      }
-
-      if (portal.light) {
-        portal.light.intensity = dimmed ? 0.3 : 2;
-      }
-
-      // Update label to show offline status
-      if (portal.labelMesh && dimmed) {
-        updatePortalLabel(portal, state);
-      }
-    }
-  }
-
-  function updatePortalLabel(portal, state) {
-    // Re-render label canvas with offline indicator
-    const labelMesh = portal.labelMesh;
-    if (!labelMesh || !labelMesh.material.map) return;
-
-    // We can't easily re-render a canvas texture each frame,
-    // so we'll use a separate overlay sprite for offline status
-    if (!portal.offlineLabel) {
-      const canvas = document.createElement('canvas');
-      canvas.width = 256;
-      canvas.height = 64;
-      const ctx = canvas.getContext('2d');
-
-      ctx.fillStyle = 'rgba(255, 68, 102, 0.8)';
-      ctx.roundRect(0, 0, 256, 64, 8);
-      ctx.fill();
-
-      ctx.fillStyle = '#ffffff';
-      ctx.font = 'bold 20px monospace';
-      ctx.textAlign = 'center';
-      ctx.textBaseline = 'middle';
-      ctx.fillText('⚠ OFFLINE', 128, 32);
-
-      const texture = new THREE.CanvasTexture(canvas);
-      const material = new THREE.SpriteMaterial({ map: texture, transparent: true });
-      const sprite = new THREE.Sprite(material);
-      sprite.scale.set(2, 0.5, 1);
-      sprite.position.y = 8.5;
-      portal.group.add(sprite);
-      portal.offlineLabel = sprite;
-    }
-
-    portal.offlineLabel.visible = state.currentOpacity < NORMAL_OPACITY * 0.5;
-  }
-
-  // ═══ Public API ═════════════════════════════════════════════
-  window.PortalHealthCheck = {
-    init(portalsRef) {
-      // Initial check
-      this.check(portalsRef, true);
-      // Periodic checks
-      if (checkTimer) clearInterval(checkTimer);
-      checkTimer = setInterval(() => this.check(portalsRef, true), CHECK_INTERVAL);
-      console.log('[PortalHealth] Initialized — checking every 5 minutes');
-    },
-
-    check(portalsRef, wsConnected) {
-      checkPortalHealth(portalsRef, wsConnected);
-    },
-
-    update(portalsRef) {
-      updatePortalVisuals(portalsRef);
-    },
-
-    getStatus() {
-      return { ...portalHealthStates };
-    },
-
-    isHealthy(portalId) {
-      return portalHealthStates[portalId]?.healthy !== false;
-    },
-
-    destroy() {
-      if (checkTimer) {
-        clearInterval(checkTimer);
-        checkTimer = null;
-      }
-    },
-  };
-})();