Assistant MCP vs Codebase Memory MCP

In-depth architectural comparison of the Assistant MCP and Codebase Memory MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Assistant MCP when:

• You need dedicated capabilities in the Knowledge & Memory domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: API Key required (BYOK (Pay Provider Direct)).
• You have access to required keys: PINECONE_API_KEY, PINECONE_ASSISTANT_HOST, LOG_LEVEL.
• Primary tools included: Pinecone Assistant information retrieval, Configurable multiple-result retrieval, Docker deployment.

Explore Assistant MCP Details

Choose Codebase Memory MCP when:

• You need dedicated capabilities in the Knowledge & Memory domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: index_repository, search_graph, query_graph.

Feature & Specification Comparison

Specification	Assistant MCP pinecone-io Knowledge & Memory	Codebase Memory MCP DeusData Knowledge & Memory
Summary	Connects to your Pinecone Assistant and gives the agent context from its knowledge engine.	Code-intelligence engine that indexes a repo into a persistent knowledge graph — functions, classes, call chains, HTTP routes, cross-service links. 159 languages via tree-sitter + Hybrid LSP, sub-ms structural queries, 99% fewer tokens than grep. Single static binary, zero dependencies, 100% local. npx codebase-memory-mcp
Category & Scope

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "pinecone-io-assistant-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "pinecone-io-assistant-mcp"
      ],
      "env": {
        "PINECONE_API_KEY": "YOUR_PINECONE_API_KEY_HERE",
        "PINECONE_ASSISTANT_HOST": "YOUR_PINECONE_ASSISTANT_HOST_HERE",
        "LOG_LEVEL": "YOUR_LOG_LEVEL_HERE"
      }
    }
  }
}

{
  "mcpServers": {
    "deusdata-codebase-memory-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "codebase-memory-mcp"
      ]
    }
  }
}

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