docs: Add documentation site and API reference

docs/index.md

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+# AegisGitea MCP - Documentation
+
+AegisGitea MCP is a security-first [Model Context Protocol (MCP)](https://modelcontextprotocol.io) server that provides controlled AI access to self-hosted Gitea repositories.
+
+## Overview
+
+AegisGitea MCP acts as a secure bridge between AI assistants (such as ChatGPT) and your Gitea instance. It exposes a limited set of read-only tools that allow an AI to browse repositories and read file contents, while enforcing strict authentication, rate limiting, and comprehensive audit logging.
+
+**Version:** 0.1.0 (Alpha)  
+**License:** MIT  
+**Requires:** Python 3.10+
+
+## Documentation
+
+| Document | Description |
+|---|---|
+| [Getting Started](getting-started.md) | Installation and first-time setup |
+| [Configuration](configuration.md) | All environment variables and settings |
+| [API Reference](api-reference.md) | HTTP endpoints and MCP tools |
+| [Architecture](architecture.md) | System design and data flow |
+| [Security](security.md) | Authentication, rate limiting, and audit logging |
+| [Deployment](deployment.md) | Docker and production deployment |
+
+## Quick Start
+
+```bash
+# 1. Clone and install
+git clone <repo-url>
+cd AegisGitea-MCP
+make install-dev
+
+# 2. Configure
+cp .env.example .env
+# Edit .env with your Gitea URL and token
+
+# 3. Generate an API key
+make generate-key
+
+# 4. Run
+make run
+```
+
+The server starts at `http://localhost:8080`.