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

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).
Restart your application – uvx automatically handles installation and execution
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 10 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

10 Languages with Tree-sitter AST Parsing: Python, JavaScript, TypeScript, Java, Kotlin, C#, Go, Objective-C, Zig, Rust
50+ File Types with Fallback Strategy: C/C++, 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

📁 Programming Languages (Click to expand)

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
Kotlin (.kt, .kts) - Package-aware symbol extraction with methods and call relationships
C# (.cs) - Namespace-aware type/member extraction with call relationships
Go (.go) - Struct methods, receiver types, and function analysis
Rust (.rs) - Functions, module-aware names, impl methods, structs/enums/traits, and basic call relationships
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)
Object-Oriented: 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

🌐 Web & Frontend (Click to expand)

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)

🗄️ Database & SQL (Click to expand)

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)

📄 Documentation & Config (Click to expand)

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

🛠️ Development Setup

For contributing or local development:

Clone and install:

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

Configure for local development:

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

Debug with MCP Inspector:

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

Alternative: Manual pip Installation

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 literal-by-default matching, optional `regex=True`, fuzzy matching, file filtering, and paginated results (10 per page by default); regex mode requires a native search tool because the basic fallback is literal-only
`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

Code Pattern Search

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

Finds: getData(), getUserData(), getFormData(), etc. Regex search is opt-in; install a native search tool and use regex=True because the basic fallback stays literal-only.

Fuzzy Function Search

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

Matches: authenticateUser, authUserToken, userAuthCheck, etc.

Language-Specific Search

Search for "API_ENDPOINT" only in Python files

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

Auto-refresh Configuration

Configure automatic index updates when files change

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

Project Maintenance

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

macOS File Watcher Options

The default FSEvents observer works well for most projects. If you experience issues, you can switch to an alternative observer via configure_file_watcher:

"auto" (default): Platform default (FSEvents on macOS)
"kqueue": Kqueue observer (macOS/BSD)
"fsevents": Force FSEvents (macOS only)
"polling": Cross-platform polling fallback

Note: Kqueue opens one file descriptor per watched file. For large projects using kqueue, you may need to increase the limit: ulimit -n 10240

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

Code Indexиндекс кода