Codebase Memory MCP vs Paper Distill MCP

In-depth architectural comparison of the Codebase Memory MCP and Paper Distill 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 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.

Explore Codebase Memory MCP Details

Choose Paper Distill 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).

Explore Paper Distill MCP Details

Feature & Specification Comparison

Specification	Codebase Memory MCP DeusData Knowledge & Memory	Paper Distill MCP Knowledge & Memory
Summary	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	Academic paper search across 11 sources with AI curation, ranked push, Zotero and Obsidian support.
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": {
    "deusdata-codebase-memory-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "codebase-memory-mcp"
      ]
    }
  }
}

{
  "mcpServers": {
    "paper-distill-mcp": {
      "command": "uvx",
      "args": [
        "paper-distill-mcp"
      ]
    }
  }
}

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