docs: make README easier to follow and update related docs (#884)

backend/docs/MCP_SERVER.md

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+# MCP (Model Context Protocol) Configuration
+
+DeerFlow supports configurable MCP servers and skills to extend its capabilities, which are loaded from a dedicated `extensions_config.json` file in the project root directory.
+
+## Setup
+
+1. Copy `extensions_config.example.json` to `extensions_config.json` in the project root directory.
+   ```bash
+   # Copy example configuration
+   cp extensions_config.example.json extensions_config.json
+   ```
+   
+2. Enable the desired MCP servers or skills by setting `"enabled": true`.
+3. Configure each server’s command, arguments, and environment variables as needed.
+4. Restart the application to load and register MCP tools.
+
+## How It Works
+
+MCP servers expose tools that are automatically discovered and integrated into DeerFlow’s agent system at runtime. Once enabled, these tools become available to agents without additional code changes.
+
+## Example Capabilities
+
+MCP servers can provide access to:
+
+- **File systems**
+- **Databases** (e.g., PostgreSQL)
+- **External APIs** (e.g., GitHub, Brave Search)
+- **Browser automation** (e.g., Puppeteer)
+- **Custom MCP server implementations**
+
+## Learn More
+
+For detailed documentation about the Model Context Protocol, visit:  
+https://modelcontextprotocol.io