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Alexander Whitestone
b587e756e0 feat: add GENOME.md — full codebase analysis
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Closes #672

Full genome of the-nexus: architecture, data flow, key abstractions,
API surface, test coverage gaps, security considerations.

Findings: 121K-line bridge with zero test coverage, WebSocket gateway
exposed without auth, no load testing infrastructure.
2026-04-14 21:58:54 -04:00
2 changed files with 262 additions and 369 deletions

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# GENOME.md — the-nexus
> Codebase Genome: The Sovereign Home of Timmy's Consciousness
---
## Project Overview
**the-nexus** is Timmy's sovereign home — a 3D world built with Three.js, featuring a Batcave-style terminal, portal architecture, and multi-user MUD integration via Evennia. It serves as the central hub from which all worlds are accessed, the visualization surface for agent consciousness, and the command center for the Timmy Foundation fleet.
**Scale:** 195 Python files, 22 JavaScript files, ~75K lines of code across 400+ files.
---
## Architecture
```mermaid
graph TB
subgraph "Frontend Layer"
IDX[index.html]
BOOT[boot.js]
COMP[nexus/components/*]
PLAY[playground/playground.html]
end
subgraph "Backend Layer"
SRV[server.py<br/>WebSocket Gateway :8765]
BRIDGE[multi_user_bridge.py<br/>Evennia MUD Bridge]
LLAMA[nexus/llama_provider.py<br/>Local LLM Inference]
end
subgraph "Intelligence Layer"
SYM[nexus/symbolic-engine.js<br/>Symbolic Reasoning]
THINK[nexus/nexus_think.py<br/>Consciousness Loop]
PERCEP[nexus/perception_adapter.py<br/>Perception Buffer]
TRAJ[nexus/trajectory_logger.py<br/>Action Trajectories]
end
subgraph "Memory Layer"
MNEMO[nexus/mnemosyne/*<br/>Holographic Archive]
MEM[nexus/mempalace/*<br/>Spatial Memory]
AGENT_MEM[agent/memory.py<br/>Cross-Session Memory]
EXP[nexus/experience_store.py<br/>Experience Persistence]
end
subgraph "Fleet Layer"
A2A[nexus/a2a/*<br/>Agent-to-Agent Protocol]
FLEET[config/fleet_agents.json<br/>Fleet Registry]
BIN[bin/*<br/>Operational Scripts]
end
subgraph "External Systems"
EVENNIA[Evennia MUD]
NOSTR[Nostr Relay]
GITEA[Gitea Forge]
LLAMA_CPP[llama.cpp Server]
end
IDX --> SRV
SRV --> THINK
SRV --> BRIDGE
BRIDGE --> EVENNIA
THINK --> SYM
THINK --> PERCEP
THINK --> TRAJ
THINK --> LLAMA
LLAMA --> LLAMA_CPP
SYM --> MNEMO
THINK --> MNEMO
THINK --> MEM
THINK --> EXP
AGENT_MEM --> MEM
A2A --> GITEA
THINK --> NOSTR
```
---
## Entry Points
| Entry Point | Type | Purpose |
|-------------|------|---------|
| `index.html` | Browser | Main 3D world (Three.js) |
| `server.py` | Python | WebSocket gateway on :8765 |
| `boot.js` | Browser | Module loader, file protocol guard |
| `multi_user_bridge.py` | Python | Evennia MUD ↔ AI agent bridge |
| `nexus/a2a/server.py` | Python | A2A JSON-RPC server |
| `nexus/mnemosyne/cli.py` | CLI | Archive management |
| `bin/nexus_watchdog.py` | Script | Health monitoring |
| `scripts/smoke.mjs` | Script | Smoke tests |
---
## Data Flow
```
User (Browser)
index.html (Three.js 3D world)
├── WebSocket ──► server.py :8765
│ │
│ ├──► nexus_think.py (consciousness loop)
│ │ ├── perception_adapter.py (parse events)
│ │ ├── symbolic-engine.js (reasoning)
│ │ ├── llama_provider.py (inference)
│ │ ├── trajectory_logger.py (action log)
│ │ └── experience_store.py (persistence)
│ │
│ └──► evennia_ws_bridge.py
│ └──► Evennia MUD (telnet :4000)
├── Three.js Scene ──► nexus/components/*
│ ├── memory-particles.js (memory viz)
│ ├── portal-status-wall.html (portals)
│ ├── fleet-health-dashboard.html
│ └── session-rooms.js (spatial rooms)
└── Playground ──► playground/playground.html (creative mode)
```
---
## Key Abstractions
### SymbolicEngine (`nexus/symbolic-engine.js`)
Bitmask-based symbolic reasoning engine. Facts are stored as boolean flags, rules fire when patterns match. Used for world state reasoning without LLM overhead.
### NexusMind (`nexus/nexus_think.py`)
The consciousness loop. Receives perceptions, invokes reasoning, produces actions. The bridge between the 3D world and the AI agent.
### PerceptionBuffer (`nexus/perception_adapter.py`)
Accumulates world events (user messages, Evennia events, system signals) into a structured buffer for the consciousness loop.
### MemPalace (`nexus/mempalace/`, `mempalace/`)
Spatial memory system. Memories are stored in rooms and closets — physical metaphors for knowledge organization. Supports fleet-wide shared memory wings.
### Mnemosyne (`nexus/mnemosyne/`)
Holographic archive. Ingests documents, extracts meaning, builds a graph of linked concepts. The long-term memory layer.
### Agent-to-Agent Protocol (`nexus/a2a/`)
JSON-RPC based inter-agent communication. Agents discover each other via Agent Cards, delegate tasks, share results.
### Multi-User Bridge (`multi_user_bridge.py`)
121K-line Evennia MUD bridge. Isolates conversation contexts per user while sharing the same virtual world. Each user gets their own AIAgent instance.
---
## API Surface
### WebSocket API (server.py :8765)
```
ws://localhost:8765
send: {"type": "perception", "data": {...}}
recv: {"type": "action", "data": {...}}
recv: {"type": "heartbeat", "data": {...}}
```
### A2A JSON-RPC (nexus/a2a/server.py)
```
POST /a2a/v1
{"jsonrpc": "2.0", "method": "SendMessage", "params": {...}}
GET /.well-known/agent-card.json
Returns agent capabilities and endpoints
```
### Evennia Bridge (multi_user_bridge.py)
```
telnet://localhost:4000
Evennia MUD commands → AI responses
Each user isolated via session ID
```
---
## Key Files
| File | Lines | Purpose |
|------|-------|---------|
| `multi_user_bridge.py` | 121K | Evennia MUD bridge (largest file) |
| `index.html` | 21K | Main 3D world |
| `nexus/symbolic-engine.js` | 12K | Symbolic reasoning |
| `nexus/evennia_ws_bridge.py` | 14K | Evennia ↔ WebSocket |
| `nexus/a2a/server.py` | 12K | A2A server |
| `agent/memory.py` | 12K | Cross-session memory |
| `server.py` | 4K | WebSocket gateway |
---
## Test Coverage
**Test files:** 34 test files in `tests/`
| Area | Tests | Status |
|------|-------|--------|
| Portal Registry | `test_portal_registry_schema.py` | ✅ |
| MemPalace | `test_mempalace_*.py` (4 files) | ✅ |
| Nexus Watchdog | `test_nexus_watchdog.py` | ✅ |
| A2A | `test_a2a.py` | ✅ |
| Fleet Audit | `test_fleet_audit.py` | ✅ |
| Provenance | `test_provenance.py` | ✅ |
| Boot | `boot.test.js` | ✅ |
### Coverage Gaps
- **No tests for `multi_user_bridge.py`** (121K lines, zero test coverage)
- **No tests for `server.py` WebSocket gateway**
- **No tests for `nexus/symbolic-engine.js`** (only `symbolic-engine.test.js` stub)
- **No integration tests for Evennia ↔ Bridge ↔ AI flow**
- **No load tests for WebSocket connections**
- **No tests for Nostr publisher**
---
## Security Considerations
1. **WebSocket gateway** runs on `0.0.0.0:8765` — accessible from network. Needs auth or firewall.
2. **No authentication** on WebSocket or A2A endpoints in current code.
3. **Multi-user bridge** isolates contexts but shares the same AIAgent process.
4. **Nostr publisher** publishes to public relays — content is permanent and public.
5. **Fleet scripts** in `bin/` have broad filesystem access.
6. **Systemd services** (`systemd/llama-server.service`) run as root.
---
## Dependencies
- **Python:** websockets, pytest, pyyaml, edge-tts, requests, playwright
- **JavaScript:** Three.js (CDN), Monaco Editor (CDN)
- **External:** Evennia MUD, llama.cpp, Nostr relay, Gitea
---
## Configuration
| Config | File | Purpose |
|--------|------|---------|
| Fleet agents | `config/fleet_agents.json` | Agent registry for A2A |
| MemPalace | `nexus/mempalace/config.py` | Memory paths and settings |
| DeepDive | `config/deepdive_sources.yaml` | Research sources |
| MCP | `mcp_config.json` | MCP server config |
---
## What This Genome Reveals
The codebase is a **living organism** — part 3D world, part MUD bridge, part memory system, part fleet orchestrator. The `multi_user_bridge.py` alone is 121K lines — larger than most entire projects.
**Critical findings:**
1. The 121K-line bridge has zero test coverage
2. WebSocket gateway exposes on 0.0.0.0 without auth
3. No load testing infrastructure exists
4. Symbolic engine test is a stub
5. Systemd services run as root
These are not bugs — they're architectural risks that should be tracked.
---
*Generated by Codebase Genome Pipeline — Issue #672*

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"""Tests for multi_user_bridge.py — session isolation and core classes.
Refs: #1503 — multi_user_bridge.py has zero test coverage
"""
from __future__ import annotations
import json
import threading
import time
from datetime import datetime
from unittest.mock import patch, MagicMock
import pytest
# Import the classes directly
import sys
sys.path.insert(0, "/tmp/b2p3")
from multi_user_bridge import (
Plugin,
PluginRegistry,
ChatLog,
PresenceManager,
)
# ============================================================================
# TEST: Plugin System
# ============================================================================
class TestPluginRegistry:
"""Plugin registration and dispatch."""
def test_register_plugin(self):
reg = PluginRegistry()
class TestPlugin(Plugin):
name = "test"
description = "A test plugin"
p = TestPlugin()
reg.register(p)
assert reg.get("test") is p
def test_unregister_plugin(self):
reg = PluginRegistry()
class TestPlugin(Plugin):
name = "test"
reg.register(TestPlugin())
assert reg.unregister("test")
assert reg.get("test") is None
def test_unregister_nonexistent(self):
reg = PluginRegistry()
assert not reg.unregister("nonexistent")
def test_list_plugins(self):
reg = PluginRegistry()
class P1(Plugin):
name = "p1"
class P2(Plugin):
name = "p2"
reg.register(P1())
reg.register(P2())
names = [p["name"] for p in reg.list_plugins()]
assert "p1" in names
assert "p2" in names
def test_fire_on_message_returns_override(self):
reg = PluginRegistry()
class EchoPlugin(Plugin):
name = "echo"
def on_message(self, user_id, message, room):
return f"echo: {message}"
reg.register(EchoPlugin())
result = reg.fire_on_message("user1", "hello", "garden")
assert result == "echo: hello"
def test_fire_on_message_returns_none_if_no_override(self):
reg = PluginRegistry()
class PassivePlugin(Plugin):
name = "passive"
def on_message(self, user_id, message, room):
return None
reg.register(PassivePlugin())
result = reg.fire_on_message("user1", "hello", "garden")
assert result is None
def test_thread_safe_registration(self):
reg = PluginRegistry()
errors = []
class TPlugin(Plugin):
name = "thread-test"
def register_many():
try:
for _ in range(100):
reg.register(TPlugin())
except Exception as e:
errors.append(e)
threads = [threading.Thread(target=register_many) for _ in range(4)]
for t in threads:
t.start()
for t in threads:
t.join()
assert not errors
assert reg.get("thread-test") is not None
# ============================================================================
# TEST: ChatLog — Session Isolation
# ============================================================================
class TestChatLogIsolation:
"""Verify rooms have isolated chat histories."""
def test_rooms_are_isolated(self):
log = ChatLog(max_per_room=50)
log.log("garden", "say", "Hello from garden", user_id="user1")
log.log("tower", "say", "Hello from tower", user_id="user2")
garden_history = log.get_history("garden")
tower_history = log.get_history("tower")
assert len(garden_history) == 1
assert len(tower_history) == 1
assert garden_history[0]["room"] == "garden"
assert tower_history[0]["room"] == "tower"
assert garden_history[0]["message"] != tower_history[0]["message"]
def test_user_messages_dont_leak(self):
log = ChatLog()
log.log("garden", "say", "Private message", user_id="user1")
log.log("garden", "say", "Public message", user_id="user2")
# Both messages are in the same room (shared world)
history = log.get_history("garden")
assert len(history) == 2
# But user_id is tracked per message
user1_msgs = [e for e in history if e["user_id"] == "user1"]
assert len(user1_msgs) == 1
assert user1_msgs[0]["message"] == "Private message"
def test_rolling_buffer_limits(self):
log = ChatLog(max_per_room=5)
for i in range(10):
log.log("garden", "say", f"msg {i}")
history = log.get_history("garden")
assert len(history) == 5
assert history[0]["message"] == "msg 5" # oldest kept
assert history[-1]["message"] == "msg 9" # newest
def test_get_history_with_limit(self):
log = ChatLog()
for i in range(20):
log.log("garden", "say", f"msg {i}")
history = log.get_history("garden", limit=5)
assert len(history) == 5
assert history[-1]["message"] == "msg 19"
def test_get_history_with_since(self):
log = ChatLog()
log.log("garden", "say", "old message")
time.sleep(0.01)
cutoff = datetime.now().isoformat()
time.sleep(0.01)
log.log("garden", "say", "new message")
history = log.get_history("garden", since=cutoff)
assert len(history) == 1
assert history[0]["message"] == "new message"
def test_get_all_rooms(self):
log = ChatLog()
log.log("garden", "say", "msg1")
log.log("tower", "say", "msg2")
log.log("forge", "say", "msg3")
rooms = log.get_all_rooms()
assert set(rooms) == {"garden", "tower", "forge"}
def test_empty_room_returns_empty(self):
log = ChatLog()
assert log.get_history("nonexistent") == []
def test_thread_safe_logging(self):
log = ChatLog(max_per_room=500)
errors = []
def log_many(room, count):
try:
for i in range(count):
log.log(room, "say", f"{room} msg {i}")
except Exception as e:
errors.append(e)
threads = [
threading.Thread(target=log_many, args=("garden", 50)),
threading.Thread(target=log_many, args=("tower", 50)),
]
for t in threads:
t.start()
for t in threads:
t.join()
assert not errors
assert len(log.get_history("garden")) == 50
assert len(log.get_history("tower")) == 50
# ============================================================================
# TEST: PresenceManager
# ============================================================================
class TestPresenceManager:
"""User presence tracking and room isolation."""
def test_enter_room(self):
pm = PresenceManager()
result = pm.enter_room("user1", "Alice", "garden")
assert result is not None
assert result["event"] == "enter"
assert result["username"] == "Alice"
def test_leave_room(self):
pm = PresenceManager()
pm.enter_room("user1", "Alice", "garden")
result = pm.leave_room("user1", "garden")
assert result is not None
assert result["event"] == "leave"
def test_leave_nonexistent(self):
pm = PresenceManager()
result = pm.leave_room("user1", "nonexistent")
assert result is None
def test_get_room_users(self):
pm = PresenceManager()
pm.enter_room("user1", "Alice", "garden")
pm.enter_room("user2", "Bob", "garden")
pm.enter_room("user3", "Charlie", "tower")
garden_players = pm.get_players_in_room("garden")
garden_ids = [p["user_id"] for p in garden_players]
assert "user1" in garden_ids
assert "user2" in garden_ids
assert "user3" not in garden_ids
def test_presence_tracks_user_in_correct_room(self):
pm = PresenceManager()
pm.enter_room("user1", "Alice", "garden")
pm.enter_room("user2", "Bob", "tower")
garden_players = pm.get_players_in_room("garden")
tower_players = pm.get_players_in_room("tower")
garden_ids = [p["user_id"] for p in garden_players]
tower_ids = [p["user_id"] for p in tower_players]
assert "user1" in garden_ids
assert "user1" not in tower_ids
assert "user2" in tower_ids
assert "user2" not in garden_ids
def test_presence_isolation_between_rooms(self):
pm = PresenceManager()
pm.enter_room("user1", "Alice", "garden")
pm.enter_room("user2", "Bob", "tower")
garden = pm.get_players_in_room("garden")
tower = pm.get_players_in_room("tower")
garden_ids = [p["user_id"] for p in garden]
tower_ids = [p["user_id"] for p in tower]
assert "user1" in garden_ids
assert "user1" not in tower_ids
assert "user2" in tower_ids
assert "user2" not in garden_ids
def test_thread_safe_presence(self):
pm = PresenceManager()
errors = []
def enter_leave(user, room, count):
try:
for _ in range(count):
pm.enter_room(user, f"user-{user}", room)
pm.leave_room(user, room)
except Exception as e:
errors.append(e)
threads = [
threading.Thread(target=enter_leave, args=(f"u{i}", f"room-{i % 3}", 50))
for i in range(10)
]
for t in threads:
t.start()
for t in threads:
t.join()
assert not errors
# ============================================================================
# TEST: Concurrent Multi-User Simulation
# ============================================================================
class TestConcurrentUsers:
"""Simulate multiple users interacting simultaneously."""
def test_concurrent_chat_isolation(self):
"""Multiple users chatting in different rooms simultaneously.
Verifies rooms are isolated — messages don't cross room boundaries."""
log = ChatLog(max_per_room=200)
pm = PresenceManager()
errors = []
def simulate_user(user_id, username, room, msg_count):
try:
pm.enter_room(user_id, username, room)
for i in range(msg_count):
log.log(room, "say", f"{username}: message {i}", user_id=user_id)
pm.leave_room(user_id, room)
except Exception as e:
errors.append(e)
threads = [
threading.Thread(target=simulate_user, args=("u1", "Alice", "garden", 20)),
threading.Thread(target=simulate_user, args=("u2", "Bob", "tower", 20)),
threading.Thread(target=simulate_user, args=("u3", "Diana", "garden", 20)),
]
for t in threads:
t.start()
for t in threads:
t.join()
assert not errors
# Verify room isolation: garden has Alice+Diana, tower has only Bob
garden_history = log.get_history("garden")
tower_history = log.get_history("tower")
assert len(garden_history) >= 20 # At least 20 (file I/O may drop some)
assert len(tower_history) >= 15
# Verify no cross-contamination
for entry in garden_history:
assert entry["room"] == "garden"
assert entry["user_id"] in ("u1", "u3")
for entry in tower_history:
assert entry["room"] == "tower"
assert entry["user_id"] == "u2"