🧠 Nucleus MCP

[!CAUTION] After the OpenClaw security crisis (1.5M API keys leaked, sleeper agents in skills), agent security is no longer optional. Nucleus was built security-first: Hypervisor controls, resource locking, and full audit trails — all 100% local.

The Universal Brain for AI Agents — One brain that syncs Cursor, Claude Desktop, Windsurf, and any MCP-compatible tool.

---

🎯 The Problem

You use multiple AI tools daily:

• Cursor for coding
• Claude Desktop for thinking
• Windsurf for exploration
• ChatGPT for quick reasoning

But they don't share memory. (Until now).

Every time you switch tools, you lose context. You re-explain decisions. You repeat yourself constantly.

---

✨ The Solution

Nucleus syncs them with one brain.

Tell Claude about a decision → Cursor knows it
Make a plan in Windsurf → Claude remembers it
One brain. All your tools.

---

🚀 What Makes Nucleus Different

Feature	Other Solutions	Nucleus
Cross-Platform Sync	Single platform only	✅ Syncs ALL your AI tools
Sovereignty	Cloud-dependent	✅ 100% local, your data stays on your machine
Protocol	Proprietary	✅ MCP standard (Anthropic-backed)
Security	Often misconfigured	✅ Secure by default, audit logs included
Lock-in	Platform-specific	✅ MIT license, open standard

---

⚡ Quick Start (2 Minutes)

1. Install

pip install nucleus-mcp

2. Initialize

nucleus-init --scan

This creates your .brain/ folder, auto-configures Claude Desktop, and automatically ingests your README.md to seed the brain with initial context.

3. Restart Claude Desktop

Then try:

"What decisions have we made about the architecture?"

Claude will now remember across sessions!

---

🔧 Manual Configuration

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS):

{
  "mcpServers": {
    "nucleus": {
      "command": "python3",
      "args": ["-m", "mcp_server_nucleus"],
      "env": {
        "NUCLEAR_BRAIN_PATH": "/path/to/your/project/.brain"
      }
    }
  }
}

Cursor

Add to ~/.cursor/mcp.json:

{
  "mcpServers": {
    "nucleus": {
      "command": "python3",
      "args": ["-m", "mcp_server_nucleus"],
      "env": {
        "NUCLEAR_BRAIN_PATH": "/path/to/your/project/.brain"
      }
    }
  }
}

Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "nucleus": {
      "command": "python3",
      "args": ["-m", "mcp_server_nucleus"],
      "env": {
        "NUCLEAR_BRAIN_PATH": "/path/to/your/project/.brain"
      }
    }
  }
}

ChatGPT (Web)

1. Go to Settings → Apps → Advanced → Developer Mode.
2. Run the Nucleus SSE Bridge: python scripts/sse_bridge.py.
3. Add http://localhost:8000/sse as your MCP endpoint.

See the Community FAQ for more details.

---

🛠 Core Tools

Memory

Tool	Description
brain_write_engram	Store persistent knowledge
brain_query_engrams	Retrieve knowledge
brain_audit_log	View decision history

Sync (Multi-Agent)

Tool	Description
brain_sync_now	Manually trigger brain sync
brain_sync_status	Check sync state and conflicts
brain_sync_auto	Enable/disable auto-sync
brain_identify_agent	Register agent identity

State Management

Tool	Description
brain_get_state	Get current project state
brain_set_state	Update project state
brain_list_artifacts	List all artifacts

Hypervisor (Security)

Tool	Description
lock_resource	Lock file/folder (immutable)
unlock_resource	Unlock resource
watch_resource	Monitor file changes
hypervisor_status	View security state

---

🔄 Multi-Agent Sync (The Killer Feature)

Multiple agents, one brain.

# Agent A (Claude Desktop) makes a decision
brain_sync_now()  # Syncs to shared .brain/

# Agent B (Cursor) automatically sees it
brain_sync_status()  # Shows last sync, active agents

Features:

• Intent-Aware Locking — Files locked with WHO/WHEN/WHY metadata
• Conflict Detection — Last-write-wins with manual resolution option
• Auto-Sync — Optional file watcher for real-time sync
• Audit Trail — Every sync logged to events.jsonl

---

⚔️ Comparison: Nucleus vs Alternatives

	OpenClaw	Claude Code	Nucleus
What it syncs	OpenClaw → OpenClaw	Claude → Claude	Everything ↔ Everything
Security	❌ Sleeper agents, key leaks	⚠️ Cloud-managed	✅ Hypervisor + audit trail
Cross-platform	❌	❌	✅
Local-first	⚠️ Some cloud	⚠️ Some cloud	✅ 100% local
Identity Persistence	❌ Session-bound	❌ Login-bound	✅ Hypervisor-enforced
MCP Native	❌ Custom protocol	⚠️ Limited	✅ Full MCP
Open Source	✅ MIT	❌ Closed	✅ MIT

OpenClaw is great for multi-agent teams on their platform. OpenClaw trades security for capability. Nucleus gives you both.

[!TIP] Check out the Detailed Comparison to see how Nucleus stacks up against ContextStream and Autonomy AI.

---

📁 The .brain/ Folder

Nucleus stores everything in a .brain/ folder in your project:

.brain/
├── config/
│   └── nucleus.yaml      # Configuration
├── ledger/
│   ├── state.json        # Current state
│   ├── events.jsonl      # Audit log
│   └── decisions.md      # Decision history
├── artifacts/
│   └── ...               # Your stored knowledge
└── sessions/
    └── ...               # Saved sessions

Your data. Your machine. Your control.

---

🤝 Contributing

We're building the universal brain for AI agents. Join us!

• 🐛 Found a bug? Open an Issue
• 💡 Feature idea? Start a Discussion
• 🔧 Want to contribute? See CONTRIBUTING.md

✨ Pioneers & Contributors

Nucleus is a community-first project. A special thank you to our first contributor for setting the standard:

• @aryasadawrate19 — Added Linux XDG support for nucleus-init, bringing Nucleus to the Linux ecosystem.

Want to be here? See CONTRIBUTING.md and claim a "Good First Issue".

Development Setup

git clone https://github.com/eidetic-works/nucleus-mcp.git
cd nucleus-mcp
python3 -m venv venv
source venv/bin/activate
pip install -e ".[dev]"
pytest tests/

🛡️ Join the Nucleus Vanguard (Private Beta)

We're building the first secure sync layer for agents. Join our Vanguard Pioneers to help shape the roadmap and get early access to features before they go public.

Join the Nucleus Vanguard (Discord) | Visit Website

[!TIP] The Vanguard is currently open for early adopters. Introduce yourself in the #welcome-start channel to claim your Vanguard Pioneer role and join the inner circle.

---

📜 License

MIT © Nucleus Team

---

⭐ Support

Star us on GitHub if Nucleus saves you from context amnesia!

One brain. All your AI tools. No more repeating yourself.

---

Built for the AI-native developer.