Nexus RAG MCP Server 🧠

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The "Second Brain" for your AI Assistant.

Configuration • Usage • Tools • Troubleshooting

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🚀 Overview

Nexus is a local Model Context Protocol (MCP) server that gives your AI agents (like Claude Desktop, Cursor, etc.) Long-Term Memory and RAG (Retrieval-Augmented Generation) capabilities.

It runs on your local machine, indexes your files, and allows your AI to:

1. Recall past conversations and decisions.
2. Search your local codebase and notes.
3. Learn your preferences over time.

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⚙️ Configuration (Zero-Setup)

You don't need to manually install Nexus. Just use uvx to run it directly from the repository.

1. Claude Desktop App

To use Nexus with Claude, add the following to your config file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "nexus": {
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/kaushikkumarkr/RAG-MCP",
        "nexus",
        "serve"
      ]
    }
  }
}

Note: This requires uv to be installed. Nexus will automatically initialize its database at ~/.nexus on the first run.

2. Cursor / Windsurf / Other IDEs

Go to Settings > Features > MCP and add a new server:

• Name: nexus
• Type: stdio
• Command: uvx --from git+https://github.com/kaushikkumarkr/RAG-MCP nexus serve

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💬 Usage Examples

Once connected, you can talk to your AI naturally. Nexus will automatically trigger the right tools.

🧠 Memory (Long-Term Storage)

User: "Remember that for the 'Financial Dashboard' project, we depend on the pandas 2.0 library and use pytest for testing."

AI: "Understood. I've saved that context for the Financial Dashboard project." (Tool used: remember)

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🔍 Retrieval (RAG)

User: "How do we handle authentication in this codebase?"

AI: "According to docs/auth_flow.md, we use JWT tokens via Auth0..." (Tool used: search_knowledge)

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⚡ Context Injection

User: "I'm starting work on the backend API. Get me up to speed."

AI: "Checking project context... Okay, for the backend API:

1. We use FastAPI.
2. The DB is Postgres.
3. Warning: Migration scripts are in /alembic." (Tool used: get_project_context)

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🛠️ Available Tools

Tool	Description	Arguments
search_knowledge	Search your local documents.	query (str), limit (int)
remember	Store a fact or memory.	content (str), project (str), tags (list)
recall	Retrieve memories.	query (str)
get_project_context	Get full overview of a project.	project (str)
get_user_preferences	Get learned user habits.	None
ingest_content	Save content from other MCPs.	content (str), source (str)
add_note	Create a markdown note.	filename (str), content (str)
list_sources	List indexed files.	None

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🛡️ Citations & Grounding

Nexus citations are precise. Every answer includes:

1. Source Path: File path (/docs/api.md).
2. Relevance: Confidence score (0-1).
3. Quote: Exact text chunk used.

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❓ Troubleshooting

Server not starting?

Run the built-in status check to verify your database and config:

nexus status

"Tool not found" error?

Ensure you have restarted your client (Claude/Cursor) after editing the config file.

How do I see what's happening?

Nexus logs to stderr. In Claude Desktop, you can open the Developer Console to see the MCP logs in real-time.

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🏗️ System Architecture

Nexus uses a Dual-Layer Cognitive Architecture that separates fast retrieval from deep understanding.

Built with: Python 3.11 • Qdrant • Sentence-Transformers • RAGAS