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2026-04-22 01:10:48 +00:00
e2299514b1 Merge branch 'main' into fix/1644
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2026-04-22 01:08:59 +00:00
Alexander Whitestone
c2003e258f docs: restore GENOME.md codebase architecture map (#1644)
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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
2026-04-20 19:16:52 -04:00
4 changed files with 234 additions and 681 deletions

234
GENOME.md Normal file
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@@ -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.*

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@@ -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/spatial-search.js"></script>
<script src="./avatar-customization.js"></script>
<script src="./lod-system.js"></script>
<script>

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/**
* Spatial Search - Find nearest user/object by name
* Issue #1540: feat: spatial search — find nearest user/object by name
*
* Provides search functionality to find users/objects by name
* and show distance, direction, and pathfinding.
*/
class SpatialSearch {
constructor(options = {}) {
this.maxDistance = options.maxDistance || 1000; // Maximum search distance
this.searchDelay = options.searchDelay || 300; // Delay before search (ms)
this.onResultSelect = options.onResultSelect || (() => {});
this.onError = options.onError || console.error;
// Track entities in the world
this.entities = new Map(); // id -> {name, position, type, ...}
// Search UI elements
this.searchInput = null;
this.resultsContainer = null;
this.pathArrow = null;
// Initialize UI
this.initUI();
}
/**
* Initialize search UI
*/
initUI() {
// Create search container
const searchContainer = document.createElement('div');
searchContainer.id = 'spatial-search-container';
searchContainer.style.cssText = `
position: fixed;
top: 20px;
left: 50%;
transform: translateX(-50%);
z-index: 1000;
display: none;
`;
// Create search input
this.searchInput = document.createElement('input');
this.searchInput.type = 'text';
this.searchInput.placeholder = 'Search users/objects...';
this.searchInput.style.cssText = `
width: 300px;
padding: 10px 15px;
border: 2px solid #4af0c0;
border-radius: 8px;
background: rgba(0, 0, 0, 0.8);
color: white;
font-size: 14px;
font-family: 'SF Mono', 'Cascadia Code', 'Fira Code', monospace;
`;
// Create results container
this.resultsContainer = document.createElement('div');
this.resultsContainer.id = 'spatial-search-results';
this.resultsContainer.style.cssText = `
max-height: 300px;
overflow-y: auto;
background: rgba(0, 0, 0, 0.9);
border: 1px solid #4af0c0;
border-radius: 8px;
margin-top: 5px;
`;
// Add event listeners
this.searchInput.addEventListener('input', () => this.handleSearch());
this.searchInput.addEventListener('keydown', (e) => this.handleKeydown(e));
// Add to container
searchContainer.appendChild(this.searchInput);
searchContainer.appendChild(this.resultsContainer);
// Add to document
document.body.appendChild(searchContainer);
// Create path arrow
this.pathArrow = document.createElement('div');
this.pathArrow.id = 'spatial-search-arrow';
this.pathArrow.style.cssText = `
position: fixed;
bottom: 100px;
right: 20px;
width: 60px;
height: 60px;
background: rgba(74, 240, 192, 0.2);
border: 2px solid #4af0c0;
border-radius: 50%;
display: none;
align-items: center;
justify-content: center;
font-size: 24px;
color: #4af0c0;
cursor: pointer;
z-index: 999;
`;
this.pathArrow.innerHTML = '→';
this.pathArrow.addEventListener('click', () => this.clearSearch());
document.body.appendChild(this.pathArrow);
}
/**
* Show search UI
*/
show() {
const container = document.getElementById('spatial-search-container');
if (container) {
container.style.display = 'block';
this.searchInput.focus();
}
}
/**
* Hide search UI
*/
hide() {
const container = document.getElementById('spatial-search-container');
if (container) {
container.style.display = 'none';
this.clearResults();
}
}
/**
* Toggle search UI
*/
toggle() {
const container = document.getElementById('spatial-search-container');
if (container) {
if (container.style.display === 'none') {
this.show();
} else {
this.hide();
}
}
}
/**
* Handle search input
*/
handleSearch() {
const query = this.searchInput.value.trim();
if (!query) {
this.clearResults();
return;
}
// Debounce search
clearTimeout(this.searchTimeout);
this.searchTimeout = setTimeout(() => {
this.performSearch(query);
}, this.searchDelay);
}
/**
* Handle keyboard events
*/
handleKeydown(event) {
if (event.key === 'Escape') {
this.hide();
} else if (event.key === 'Enter') {
const firstResult = this.resultsContainer.querySelector('.search-result');
if (firstResult) {
firstResult.click();
}
}
}
/**
* Perform search
*/
performSearch(query) {
const results = this.searchEntities(query);
this.displayResults(results);
}
/**
* Search entities by name
*/
searchEntities(query) {
const lowerQuery = query.toLowerCase();
const results = [];
for (const [id, entity] of this.entities) {
const name = (entity.name || '').toLowerCase();
const type = (entity.type || '').toLowerCase();
// Check if name or type matches query
if (name.includes(lowerQuery) || type.includes(lowerQuery)) {
results.push({
id,
name: entity.name,
type: entity.type,
position: entity.position,
distance: this.calculateDistance(entity.position),
direction: this.calculateDirection(entity.position)
});
}
}
// Sort by distance
results.sort((a, b) => a.distance - b.distance);
// Limit results
return results.slice(0, 10);
}
/**
* Calculate distance to entity
*/
calculateDistance(position) {
if (!position) return Infinity;
// Get local player position (would be from game state)
const localPos = this.getLocalPlayerPosition();
if (!localPos) return Infinity;
const dx = position.x - localPos.x;
const dy = position.y - localPos.y;
const dz = position.z - localPos.z;
return Math.sqrt(dx * dx + dy * dy + dz * dz);
}
/**
* Calculate direction to entity
*/
calculateDirection(position) {
if (!position) return 'unknown';
const localPos = this.getLocalPlayerPosition();
if (!localPos) return 'unknown';
const dx = position.x - localPos.x;
const dz = position.z - localPos.z;
// Calculate angle
const angle = Math.atan2(dz, dx) * (180 / Math.PI);
// Convert to direction
if (angle >= -22.5 && angle < 22.5) return 'E';
if (angle >= 22.5 && angle < 67.5) return 'SE';
if (angle >= 67.5 && angle < 112.5) return 'S';
if (angle >= 112.5 && angle < 157.5) return 'SW';
if (angle >= 157.5 || angle < -157.5) return 'W';
if (angle >= -157.5 && angle < -112.5) return 'NW';
if (angle >= -112.5 && angle < -67.5) return 'N';
if (angle >= -67.5 && angle < -22.5) return 'NE';
return 'unknown';
}
/**
* Get local player position (placeholder)
*/
getLocalPlayerPosition() {
// In real implementation, this would get position from game state
// For now, return a placeholder
return { x: 0, y: 0, z: 0 };
}
/**
* Display search results
*/
displayResults(results) {
this.clearResults();
if (results.length === 0) {
const noResults = document.createElement('div');
noResults.className = 'search-no-results';
noResults.textContent = 'No results found';
noResults.style.cssText = `
padding: 10px;
color: #888;
font-style: italic;
`;
this.resultsContainer.appendChild(noResults);
return;
}
for (const result of results) {
const resultElement = this.createResultElement(result);
this.resultsContainer.appendChild(resultElement);
}
}
/**
* Create result element
*/
createResultElement(result) {
const element = document.createElement('div');
element.className = 'search-result';
element.style.cssText = `
padding: 10px 15px;
border-bottom: 1px solid rgba(74, 240, 192, 0.2);
cursor: pointer;
display: flex;
justify-content: space-between;
align-items: center;
`;
element.innerHTML = `
<div>
<div style="font-weight: bold; color: #4af0c0;">${result.name}</div>
<div style="font-size: 12px; color: #888;">${result.type || 'Unknown'}</div>
</div>
<div style="text-align: right;">
<div style="color: #4af0c0;">${result.distance.toFixed(1)}m</div>
<div style="font-size: 12px; color: #888;">${result.direction}</div>
</div>
`;
element.addEventListener('click', () => {
this.selectResult(result);
});
return element;
}
/**
* Select a search result
*/
selectResult(result) {
console.log('[SpatialSearch] Selected:', result);
// Show path arrow
this.showPathArrow(result);
// Call callback
this.onResultSelect(result);
// Hide search
this.hide();
}
/**
* Show path arrow pointing to result
*/
showPathArrow(result) {
if (!this.pathArrow) return;
// Update arrow direction
const arrow = this.pathArrow.querySelector('span') || this.pathArrow;
const directionArrows = {
'N': '↑',
'NE': '↗',
'E': '→',
'SE': '↘',
'S': '↓',
'SW': '↙',
'W': '←',
'NW': '↖'
};
arrow.innerHTML = directionArrows[result.direction] || '?';
// Show arrow
this.pathArrow.style.display = 'flex';
// Update title
this.pathArrow.title = `${result.name} - ${result.distance.toFixed(1)}m ${result.direction}`;
}
/**
* Clear search results
*/
clearResults() {
if (this.resultsContainer) {
this.resultsContainer.innerHTML = '';
}
}
/**
* Clear search and hide arrow
*/
clearSearch() {
this.clearResults();
this.searchInput.value = '';
if (this.pathArrow) {
this.pathArrow.style.display = 'none';
}
}
/**
* Register an entity
*/
registerEntity(id, entity) {
this.entities.set(id, entity);
}
/**
* Unregister an entity
*/
unregisterEntity(id) {
this.entities.delete(id);
}
/**
* Update entity position
*/
updateEntityPosition(id, position) {
const entity = this.entities.get(id);
if (entity) {
entity.position = position;
}
}
/**
* Get search status
*/
getStatus() {
return {
entityCount: this.entities.size,
maxDistance: this.maxDistance,
searchDelay: this.searchDelay
};
}
}
// Export for use in other modules
if (typeof module !== 'undefined' && module.exports) {
module.exports = SpatialSearch;
}
// Global instance for browser use
if (typeof window !== 'undefined') {
window.SpatialSearch = SpatialSearch;
// Auto-initialize
document.addEventListener('DOMContentLoaded', () => {
const search = new SpatialSearch({
maxDistance: 1000,
onResultSelect: (result) => {
console.log('Selected:', result);
// In real implementation, this would navigate to the entity
}
});
// Store globally
window.spatialSearch = search;
// Add keyboard shortcut (Ctrl+F or Cmd+F)
document.addEventListener('keydown', (e) => {
if ((e.ctrlKey || e.metaKey) && e.key === 'f') {
e.preventDefault();
search.toggle();
}
});
});
}

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@@ -1,223 +0,0 @@
/**
* Tests for Spatial Search
* Issue #1540: feat: spatial search — find nearest user/object by name
*/
const test = require('node:test');
const assert = require('node:assert/strict');
const fs = require('node:fs');
const path = require('node:path');
const ROOT = path.resolve(__dirname, '..');
// Mock document
const mockDocument = {
createElement: (tag) => {
const element = {
style: {},
innerHTML: '',
textContent: '',
placeholder: '',
title: '',
addEventListener: () => {},
appendChild: () => {},
querySelector: () => null,
querySelectorAll: () => [],
focus: () => {}
};
return element;
},
body: {
appendChild: () => {}
},
getElementById: () => null,
addEventListener: () => {}
};
// Mock console
const mockConsole = {
log: () => {},
warn: () => {},
error: () => {}
};
// Load spatial-search.js
const spatialSearchPath = path.join(ROOT, 'js', 'spatial-search.js');
const spatialSearchCode = fs.readFileSync(spatialSearchPath, 'utf8');
// Create VM context
const context = {
module: { exports: {} },
exports: {},
console: mockConsole,
document: mockDocument,
window: {
addEventListener: () => {},
location: { protocol: 'http:', hostname: 'localhost' }
},
Math: Math,
setTimeout: () => {},
clearTimeout: () => {}
};
// Execute spatial-search.js in context
const vm = require('node:vm');
vm.runInNewContext(spatialSearchCode, context);
// Get SpatialSearch class
const SpatialSearch = context.window.SpatialSearch || context.module.exports;
test('SpatialSearch loads correctly', () => {
assert.ok(SpatialSearch, 'SpatialSearch should be defined');
assert.ok(typeof SpatialSearch === 'function', 'SpatialSearch should be a constructor');
});
test('SpatialSearch can be instantiated', () => {
const search = new SpatialSearch();
assert.ok(search, 'SpatialSearch instance should be created');
assert.equal(search.maxDistance, 1000, 'Should have default max distance');
assert.equal(search.searchDelay, 300, 'Should have default search delay');
assert.ok(search.entities, 'Should have entities Map');
});
test('SpatialSearch can register entities', () => {
const search = new SpatialSearch();
search.registerEntity('user1', {
name: 'Alice',
type: 'user',
position: { x: 10, y: 0, z: 5 }
});
search.registerEntity('user2', {
name: 'Bob',
type: 'user',
position: { x: 20, y: 0, z: 10 }
});
assert.equal(search.entities.size, 2, 'Should have 2 entities');
assert.ok(search.entities.get('user1'), 'Should have user1');
assert.ok(search.entities.get('user2'), 'Should have user2');
});
test('SpatialSearch can unregister entities', () => {
const search = new SpatialSearch();
search.registerEntity('user1', { name: 'Alice', type: 'user' });
search.registerEntity('user2', { name: 'Bob', type: 'user' });
assert.equal(search.entities.size, 2, 'Should have 2 entities');
search.unregisterEntity('user1');
assert.equal(search.entities.size, 1, 'Should have 1 entity after unregister');
assert.ok(!search.entities.get('user1'), 'Should not have user1');
});
test('SpatialSearch can update entity position', () => {
const search = new SpatialSearch();
search.registerEntity('user1', {
name: 'Alice',
type: 'user',
position: { x: 10, y: 0, z: 5 }
});
const newPos = { x: 15, y: 0, z: 10 };
search.updateEntityPosition('user1', newPos);
const entity = search.entities.get('user1');
assert.deepEqual(entity.position, newPos, 'Should update position');
});
test('SpatialSearch calculates distance correctly', () => {
const search = new SpatialSearch();
// Mock getLocalPlayerPosition
search.getLocalPlayerPosition = () => ({ x: 0, y: 0, z: 0 });
const pos1 = { x: 3, y: 0, z: 4 };
const distance1 = search.calculateDistance(pos1);
assert.equal(distance1, 5, 'Should calculate 3-4-5 triangle correctly');
const pos2 = { x: 0, y: 0, z: 0 };
const distance2 = search.calculateDistance(pos2);
assert.equal(distance2, 0, 'Should be 0 at same position');
});
test('SpatialSearch calculates direction correctly', () => {
const search = new SpatialSearch();
// Mock getLocalPlayerPosition
search.getLocalPlayerPosition = () => ({ x: 0, y: 0, z: 0 });
// Test different directions
assert.equal(search.calculateDirection({ x: 10, y: 0, z: 0 }), 'E', 'Should be East');
assert.equal(search.calculateDirection({ x: 0, y: 0, z: 10 }), 'S', 'Should be South');
assert.equal(search.calculateDirection({ x: -10, y: 0, z: 0 }), 'W', 'Should be West');
assert.equal(search.calculateDirection({ x: 0, y: 0, z: -10 }), 'N', 'Should be North');
});
test('SpatialSearch searches entities correctly', () => {
const search = new SpatialSearch();
// Mock getLocalPlayerPosition
search.getLocalPlayerPosition = () => ({ x: 0, y: 0, z: 0 });
// Register entities
search.registerEntity('user1', {
name: 'Alice',
type: 'user',
position: { x: 10, y: 0, z: 0 }
});
search.registerEntity('user2', {
name: 'Bob',
type: 'user',
position: { x: 20, y: 0, z: 0 }
});
search.registerEntity('obj1', {
name: 'Apple',
type: 'object',
position: { x: 5, y: 0, z: 0 }
});
// Search for 'ali'
const results1 = search.searchEntities('ali');
assert.equal(results1.length, 1, 'Should find 1 result for "ali"');
assert.equal(results1[0].name, 'Alice', 'Should find Alice');
// Search for 'bob'
const results2 = search.searchEntities('bob');
assert.equal(results2.length, 1, 'Should find 1 result for "bob"');
assert.equal(results2[0].name, 'Bob', 'Should find Bob');
// Search for 'user' (type)
const results3 = search.searchEntities('user');
assert.equal(results3.length, 2, 'Should find 2 results for "user"');
// Search for 'apple'
const results4 = search.searchEntities('apple');
assert.equal(results4.length, 1, 'Should find 1 result for "apple"');
assert.equal(results4[0].name, 'Apple', 'Should find Apple');
// Search for non-existent
const results5 = search.searchEntities('xyz');
assert.equal(results5.length, 0, 'Should find 0 results for "xyz"');
});
test('SpatialSearch gets status', () => {
const search = new SpatialSearch();
search.registerEntity('user1', { name: 'Alice', type: 'user' });
search.registerEntity('user2', { name: 'Bob', type: 'user' });
const status = search.getStatus();
assert.ok(status, 'Should return status object');
assert.equal(status.entityCount, 2, 'Should have 2 entities');
assert.equal(status.maxDistance, 1000, 'Should have correct max distance');
assert.equal(status.searchDelay, 300, 'Should have correct search delay');
});
console.log('All SpatialSearch tests passed!');