Code Index MCP for Claude Code: Setup & Config

What you can do with Code Index in Claude Code

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

• Summarize imports, functions, and complexity after deep indexing.
• Explore an unfamiliar repository during a code review.
• Keep file discovery current as the workspace changes.

Before you start: Code Index in Claude Code

• 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 Code configuration

1. Choose Claude Code configuration scope

   For Code Index MCP, open Project scope: .mcp.json at the repository root. Project JSON: merge into mcpServers; user scope: use the CLI.

2. Add Code Index MCP to Claude Code

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

3. Check Code Index MCP in Claude Code

   Code Index MCP: Inspect claude mcp list and /mcp status.

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

claude mcp add-json --scope project 'code-index-mcp' '{"type":"stdio","command":"uvx","args":["code-index-mcp"],"env":{}}'

Code Index tools available to Claude Code

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

set_project_path

For Code Index's set_project_path, review the permission request and arguments in Claude Code before approval.

refresh_index

For Code Index's refresh_index, review the permission request and arguments in Claude Code before approval.

build_deep_index

For Code Index's build_deep_index, review the permission request and arguments in Claude Code before approval.

Build symbol metadata needed for deep analysis.

get_settings_info

For Code Index's get_settings_info, review the permission request and arguments in Claude Code before approval.

Inspect project configuration and indexing status.

search_code_advanced

For Code Index's search_code_advanced, review the permission request and arguments in Claude Code before approval.

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

find_files

For Code Index's find_files, review the permission request and arguments in Claude Code before approval.

Find repository files using glob patterns.

get_file_summary

For Code Index's get_file_summary, review the permission request and arguments in Claude Code before approval.

get_file_watcher_status

For Code Index's get_file_watcher_status, review the permission request and arguments in Claude Code before approval.

configure_file_watcher

For Code Index's configure_file_watcher, review the permission request and arguments in Claude Code before approval.

create_temp_directory

For Code Index's create_temp_directory, review the permission request and arguments in Claude Code before approval.

check_temp_directory

For Code Index's check_temp_directory, review the permission request and arguments in Claude Code before approval.

Check index storage location and permissions.

clear_settings

For Code Index's clear_settings, review the permission request and arguments in Claude Code before approval.

Reset cached index data and configuration.

refresh_search_tools

For Code Index's refresh_search_tools, review the permission request and arguments in Claude Code before approval.

Detect available native search utilities again.

Code Index: full stored tool descriptions

Troubleshooting Code Index in Claude Code

• If Code Index MCP fails to start, check uvx code-index-mcp (from uv, for Python tools), the working directory, and Claude Code's selected scope; inspect claude mcp list and /mcp.
• Code Index MCP uses stdio here: Claude Code 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 Code troubleshooting lives in the /clients/claude-code guide.

Frequently asked questions