The code-index-mcp repository implements a Model Context Protocol (MCP) server that provides code indexing and analysis capabilities for Large Language Models (LLMs). It enables AI assistants to query codebases for symbol definitions, call relationships, file contents, and project metadata through a standardized MCP interface. The system features a three-layer architecture separating technical tools (file system, search, monitoring), business services (code intelligence, index management, project management), and MCP entry points. It supports shallow indexing (file discovery) and deep indexing (symbol extraction via tree-sitter AST parsers) for over 10 programming languages, with SQLite persistence for indexes and real-time file watching for automatic updates. The application is designed for integration with MCP-compatible clients like Claude Desktop and Codex CLI.