fix: Docker stdio communication for Claude Desktop compatibility

Fixed the initialization timeout issue with minimal changes:

1. Added stdout flush after server connection to combat Docker buffering
2. Fixed docker-entrypoint.sh to not output to stdout in stdio mode
3. Added process.stdin.resume() to keep server alive
4. Added IS_DOCKER environment variable for future use
5. Updated README to prioritize Docker with correct -i flag configuration

The core issue was Docker's block buffering preventing immediate JSON-RPC
responses. The -i flag maintains stdin connection, and explicit flushing
ensures responses reach Claude Desktop immediately.

Also fixed "Shutting down..." message that was breaking JSON-RPC protocol
by redirecting it to stderr in stdio mode.

Docker is now the recommended installation method as originally intended.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/mcp/server-update.ts

@@ -912,6 +912,17 @@ Full documentation is being prepared. For now, use get_node_essentials for confi
     
     const transport = new StdioServerTransport();
     await this.server.connect(transport);
+    
+    // Force flush stdout for Docker environments
+    // Docker uses block buffering which can delay MCP responses
+    if (!process.stdout.isTTY) {
+      // Write empty string to force flush
+      process.stdout.write('', () => {});
+    }
+    
     logger.info('n8n Documentation MCP Server running on stdio transport');
+    
+    // Keep the process alive and listening
+    process.stdin.resume();
   }
 }