Code Index MCP for Claude Desktop: Setup & Config

What you can do with Code Index in Claude Desktop

Use quick file indexing and opt-in deep syntax analysis to help assistants navigate larger repositories.

• Find code affected by an API migration.
• Locate files by glob before inspecting them.
• Summarize imports, functions, and complexity after deep indexing.

Before you start: Code Index in Claude Desktop

• Python 3.10+
• uv / uvx
• A project directory to index
• A native search utility for regex mode

Call set_project_path after launch or use the documented --project-path option. File watching refreshes the shallow index; build_deep_index is required for symbol summaries. Windows clients may need the profile-directory environment overrides described in the README.

Code Index Claude Desktop configuration

1. Choose Claude Desktop configuration scope

   For Code Index MCP, open macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json. Merge under mcpServers via Settings → Developer → Edit Config when available.

2. Add Code Index MCP to Claude Desktop

   Use the code-index-mcp entry below in mcpServers. Keep Code Index MCP's documented stdio connection fields and your other Claude Desktop entries.

3. Check Code Index MCP in Claude Desktop

   Code Index MCP: Fully quit and reopen Claude Desktop; check developer diagnostics.

{
  "mcpServers": {
    "code-index-mcp": {
      "command": "uvx",
      "args": [
        "code-index-mcp"
      ],
      "env": {}
    }
  }
}

Code Index tools available to Claude Desktop

Code Index's stored tool list documents 13 tools; compare it with Claude Desktop's connected tool list, because the stored list is not a live check.

set_project_path

When Claude Desktop requests set_project_path from Code Index, review the action before approving it.

Choose a repository directory and initialize its index.

refresh_index

When Claude Desktop requests refresh_index from Code Index, review the action before approving it.

Rebuild the shallow file index.

build_deep_index

When Claude Desktop requests build_deep_index from Code Index, review the action before approving it.

Build symbol metadata needed for deep analysis.

get_settings_info

When Claude Desktop requests get_settings_info from Code Index, review the action before approving it.

Inspect project configuration and indexing status.

search_code_advanced

When Claude Desktop requests search_code_advanced from Code Index, review the action before approving it.

Search code with filters, pagination, and optional fuzzy or regex matching.

find_files

When Claude Desktop requests find_files from Code Index, review the action before approving it.

Find repository files using glob patterns.

get_file_summary

When Claude Desktop requests get_file_summary from Code Index, review the action before approving it.

Summarize file structure and symbols using the deep index.

get_file_watcher_status

When Claude Desktop requests get_file_watcher_status from Code Index, review the action before approving it.

configure_file_watcher

When Claude Desktop requests configure_file_watcher from Code Index, review the action before approving it.

create_temp_directory

When Claude Desktop requests create_temp_directory from Code Index, review the action before approving it.

check_temp_directory

When Claude Desktop requests check_temp_directory from Code Index, review the action before approving it.

clear_settings

When Claude Desktop requests clear_settings from Code Index, review the action before approving it.

refresh_search_tools

When Claude Desktop requests refresh_search_tools from Code Index, review the action before approving it.

Code Index: full stored tool descriptions

Troubleshooting Code Index in Claude Desktop

• Fully quit and reopen Claude Desktop for Code Index MCP. If uvx code-index-mcp (from uv, for Python tools) is missing, check the desktop process's PATH, which may differ from your terminal.
• Code Index MCP uses stdio here: Claude Desktop must keep the configured process running; protocol output belongs on stdout and diagnostics on stderr.
• Known limitation: Deep summaries require build_deep_index first.
• Known limitation: Languages outside the specialized set get basic fallback indexing.
• Known limitation: Regex search requires an installed native search utility.
• General Claude Desktop troubleshooting lives in the /clients/claude-desktop guide.

Frequently asked questions