Code Index MCP

Intelligent code indexing and analysis for Large Language Models

Transform how AI understands your codebase with advanced search, analysis, and navigation capabilities.

Overview

Code Index MCP is a Model Context Protocol server that bridges the gap between AI models and complex codebases. It provides intelligent indexing, advanced search capabilities, and detailed code analysis to help AI assistants understand and navigate your projects effectively.

Perfect for: Code review, refactoring, documentation generation, debugging assistance, and architectural analysis.

Quick Start

🚀 Recommended Setup (Most Users)

The easiest way to get started with any MCP-compatible application:

Prerequisites: Python 3.10+ and uv

1. Add to your MCP configuration (e.g., claude_desktop_config.json or ~/.claude.json):

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

   Optional: append --project-path /absolute/path/to/repo to the args array so the server initializes with that repository automatically (equivalent to calling set_project_path after startup).

2. Restart your application – uvx automatically handles installation and execution

3. Start using (give these prompts to your AI assistant):

   Set the project path to /Users/dev/my-react-app
   Find all TypeScript files in this project  
   Search for "authentication" functions
   Analyze the main App.tsx file
   

   If you launch with --project-path, you can skip the first command above - the server already knows the project location.

Codex CLI Configuration

If you are using Anthropic's Codex CLI, add the server to ~/.codex/config.toml. On Windows the file lives at C:\Users\<you>\.codex\config.toml:

[mcp_servers.code-index]
type = "stdio"
command = "uvx"
args = ["code-index-mcp"]

You can append --project-path C:/absolute/path/to/repo to the args list to set the project automatically on startup (same effect as running the set_project_path tool).

On Windows, uvx needs the standard profile directories to be present. Keep the environment override in the same block so the MCP starts reliably:

env = {
  HOME = "C:\\Users\\<you>",
  APPDATA = "C:\\Users\\<you>\\AppData\\Roaming",
  LOCALAPPDATA = "C:\\Users\\<you>\\AppData\\Local",
  SystemRoot = "C:\\Windows"
}

Linux and macOS already expose the required XDG paths and HOME, so you can usually omit the env table there. Add overrides only if you run the CLI inside a restricted container.

FastMCP & Discovery Manifests

• Run fastmcp run fastmcp.json to launch the server via FastMCP with the correct source entrypoint and dependency metadata. Pass --project-path (or call the set_project_path tool after startup) so the index boots against the right repository.
• Serve or copy .well-known/mcp.json to share a standards-compliant MCP manifest. Clients that support the .well-known convention (e.g., Claude Desktop, Codex CLI) can import this file directly instead of crafting configs manually.
• Publish .well-known/mcp.llmfeed.json when you want to expose the richer LLM Feed metadata. It references the same code-index server definition plus documentation/source links, which helps registries present descriptions, tags, and capabilities automatically.

When sharing the manifests, remind consumers to supply --project-path (or to call set_project_path) so the server indexes the intended repository.

Typical Use Cases

Code Review: "Find all places using the old API"
Refactoring Help: "Where is this function called?"
Learning Projects: "Show me the main components of this React project"
Debugging: "Search for all error handling related code"

Key Features

🔍 Intelligent Search & Analysis

• Dual-Strategy Architecture: Specialized tree-sitter parsing for 7 core languages, fallback strategy for 50+ file types
• Direct Tree-sitter Integration: No regex fallbacks for specialized languages - fail fast with clear errors
• Advanced Search: Auto-detects and uses the best available tool (ugrep, ripgrep, ag, or grep)
• Universal File Support: Comprehensive coverage from advanced AST parsing to basic file indexing
• File Analysis: Deep insights into structure, imports, classes, methods, and complexity metrics after running build_deep_index

🗂️ Multi-Language Support

• 7 Languages with Tree-sitter AST Parsing: Python, JavaScript, TypeScript, Java, Go, Objective-C, Zig
• 50+ File Types with Fallback Strategy: C/C++, Rust, Ruby, PHP, and all other programming languages
• Document & Config Files: Markdown, JSON, YAML, XML with appropriate handling
• Web Frontend: Vue, React, Svelte, HTML, CSS, SCSS
• Java Web & Build: JSP/Tag files (.jsp, .jspx, .jspf, .tag, .tagx), Grails/GSP (.gsp), Gradle & Groovy builds (.gradle, .groovy), .properties, and Protocol Buffers (.proto)
• Database: SQL variants, NoSQL, stored procedures, migrations
• Configuration: JSON, YAML, XML, Markdown
• View complete list

⚡ Real-time Monitoring & Auto-refresh

• File Watcher: Automatic index updates when files change
• Cross-platform: Native OS file system monitoring
• Smart Processing: Batches rapid changes to prevent excessive rebuilds
• Shallow Index Refresh: Watches file changes and keeps the file list current; run a deep rebuild when you need symbol metadata

⚡ Performance & Efficiency

• Tree-sitter AST Parsing: Native syntax parsing for accurate symbol extraction
• Persistent Caching: Stores indexes for lightning-fast subsequent access
• Smart Filtering: Intelligent exclusion of build directories and temporary files
• Memory Efficient: Optimized for large codebases
• Direct Dependencies: No fallback mechanisms - fail fast with clear error messages

Supported File Types

Languages with Specialized Tree-sitter Strategies:

• Python (.py, .pyw) - Full AST analysis with class/method extraction and call tracking
• JavaScript (.js, .jsx, .mjs, .cjs) - ES6+ class and function parsing with tree-sitter
• TypeScript (.ts, .tsx) - Complete type-aware symbol extraction with interfaces
• Java (.java) - Full class hierarchy, method signatures, and call relationships
• Go (.go) - Struct methods, receiver types, and function analysis
• Objective-C (.m, .mm) - Class/instance method distinction with +/- notation
• Zig (.zig, .zon) - Function and struct parsing with tree-sitter AST

All Other Programming Languages: All other programming languages use the FallbackParsingStrategy which provides basic file indexing and metadata extraction. This includes:

• System & Low-Level: C/C++ (.c, .cpp, .h, .hpp), Rust (.rs)
• Object-Oriented: C# (.cs), Kotlin (.kt), Scala (.scala), Swift (.swift)
• Scripting & Dynamic: Ruby (.rb), PHP (.php), Shell (.sh, .bash)
• And 40+ more file types - All handled through the fallback strategy for basic indexing

Frameworks & Libraries:

• Vue (.vue)
• Svelte (.svelte)
• Astro (.astro)

Styling:

• CSS (.css, .scss, .less, .sass, .stylus, .styl)
• HTML (.html)

Templates:

• Handlebars (.hbs, .handlebars)
• EJS (.ejs)
• Pug (.pug)
• FreeMarker (.ftl)
• Mustache (.mustache)
• Liquid (.liquid)
• ERB (.erb)

SQL Variants:

• Standard SQL (.sql, .ddl, .dml)
• Database-specific (.mysql, .postgresql, .psql, .sqlite, .mssql, .oracle, .ora, .db2)

Database Objects:

• Procedures & Functions (.proc, .procedure, .func, .function)
• Views & Triggers (.view, .trigger, .index)

Migration & Tools:

• Migration files (.migration, .seed, .fixture, .schema)
• Tool-specific (.liquibase, .flyway)

NoSQL & Modern:

• Graph & Query (.cql, .cypher, .sparql, .gql)

• Markdown (.md, .mdx)
• Configuration (.json, .xml, .yml, .yaml, .properties)

🛠️ Development Setup

For contributing or local development:

1. Clone and install:

   git clone https://github.com/johnhuang316/code-index-mcp.git
   cd code-index-mcp
   uv sync
   

2. Configure for local development:

   {
     "mcpServers": {
       "code-index": {
         "command": "uv",
         "args": ["run", "code-index-mcp"]
       }
     }
   }
   

3. Debug with MCP Inspector:

   npx @modelcontextprotocol/inspector uv run code-index-mcp
   

If you prefer traditional pip management:

pip install code-index-mcp

Then configure:

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

Available Tools

🏗️ Project Management

Tool	Description
set_project_path	Initialize indexing for a project directory
refresh_index	Rebuild the shallow file index after file changes
build_deep_index	Generate the full symbol index used by deep analysis
get_settings_info	View current project configuration and status

Run build_deep_index when you need symbol-level data; the default shallow index powers quick file discovery.

🔍 Search & Discovery

Tool	Description
search_code_advanced	Smart search with regex, fuzzy matching, file filtering, and paginated results (10 per page by default)
find_files	Locate files using glob patterns (e.g., **/*.py)
get_file_summary	Analyze file structure, functions, imports, and complexity (requires deep index)

🔄 Monitoring & Auto-refresh

Tool	Description
get_file_watcher_status	Check file watcher status and configuration
configure_file_watcher	Enable/disable auto-refresh and configure settings

🛠️ System & Maintenance

Tool	Description
create_temp_directory	Set up storage directory for index data
check_temp_directory	Verify index storage location and permissions
clear_settings	Reset all cached data and configurations
refresh_search_tools	Re-detect available search tools (ugrep, ripgrep, etc.)

Usage Examples

🎯 Quick Start Workflow

1. Initialize Your Project

Set the project path to /Users/dev/my-react-app

Automatically indexes your codebase and creates searchable cache

2. Explore Project Structure

Find all TypeScript component files in src/components

Uses: find_files with pattern src/components/**/*.tsx

3. Analyze Key Files

Give me a summary of src/api/userService.ts

Uses: get_file_summary to show functions, imports, and complexity Tip: run build_deep_index first if you get a needs_deep_index response.

🔍 Advanced Search Examples

Search for all function calls matching "get.*Data" using regex

Finds: getData(), getUserData(), getFormData(), etc.

Find authentication-related functions with fuzzy search for 'authUser'

Matches: authenticateUser, authUserToken, userAuthCheck, etc.

Search for "API_ENDPOINT" only in Python files

Uses: search_code_advanced with file_pattern: "*.py" (defaults to 10 matches; use max_results to expand or start_index to page)

Configure automatic index updates when files change

Uses: configure_file_watcher to enable/disable monitoring and set debounce timing

I added new components, please refresh the project index

Uses: refresh_index to update the searchable cache

Troubleshooting

🔄 Auto-refresh Not Working

If automatic index updates aren't working when files change, try:

• pip install watchdog (may resolve environment isolation issues)
• Use manual refresh: Call the refresh_index tool after making file changes
• Check file watcher status: Use get_file_watcher_status to verify monitoring is active

Development & Contributing

🔧 Building from Source

git clone https://github.com/johnhuang316/code-index-mcp.git
cd code-index-mcp
uv sync
uv run code-index-mcp

🐛 Debugging

npx @modelcontextprotocol/inspector uvx code-index-mcp

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

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📜 License

MIT License

🌐 Translations

• 繁體中文
• 日本語