fix: resolve Docker stdio initialization timeout issue

- Add InitializeRequestSchema handler to MCP server
- Implement stdout flushing for Docker environments
- Create stdio-wrapper for clean JSON-RPC communication
- Update docker-entrypoint.sh to prevent stdout pollution
- Fix logger to check MCP_MODE before level check

These changes ensure the MCP server responds to initialization requests
within Claude Desktop's 60-second timeout when running in Docker.

src/mcp/server-update.ts

@@ -3,6 +3,7 @@ import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
 import { 
   CallToolRequestSchema, 
   ListToolsRequestSchema,
+  InitializeRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js';
 import { existsSync } from 'fs';
 import path from 'path';
@@ -102,6 +103,27 @@ export class N8NDocumentationMCPServer {
   }
 
   private setupHandlers(): void {
+    // Handle initialization
+    this.server.setRequestHandler(InitializeRequestSchema, async () => {
+      const response = {
+        protocolVersion: '2024-11-05',
+        capabilities: {
+          tools: {},
+        },
+        serverInfo: {
+          name: 'n8n-documentation-mcp',
+          version: '2.4.1',
+        },
+      };
+      
+      // Debug: Log to stderr to see if handler is called
+      if (process.env.DEBUG_MCP === 'true') {
+        console.error('Initialize handler called, returning:', JSON.stringify(response));
+      }
+      
+      return response;
+    });
+
     // Handle tool listing
     this.server.setRequestHandler(ListToolsRequestSchema, async () => ({
       tools: n8nDocumentationToolsFinal,
@@ -915,9 +937,15 @@ Full documentation is being prepared. For now, use get_node_essentials for confi
     
     // 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('', () => {});
+    if (!process.stdout.isTTY || process.env.IS_DOCKER) {
+      // Override write to auto-flush
+      const originalWrite = process.stdout.write.bind(process.stdout);
+      process.stdout.write = function(chunk: any, encoding?: any, callback?: any) {
+        const result = originalWrite(chunk, encoding, callback);
+        // Force immediate flush
+        process.stdout.emit('drain');
+        return result;
+      };
     }
     
     logger.info('n8n Documentation MCP Server running on stdio transport');

src/mcp/stdio-wrapper.ts

@@ -0,0 +1,52 @@
+#!/usr/bin/env node
+
+/**
+ * Stdio wrapper for MCP server
+ * Ensures clean JSON-RPC communication by suppressing all non-JSON output
+ */
+
+// Suppress all console output before anything else
+const originalConsoleLog = console.log;
+const originalConsoleError = console.error;
+const originalConsoleWarn = console.warn;
+const originalConsoleInfo = console.info;
+const originalConsoleDebug = console.debug;
+
+// Override all console methods
+console.log = () => {};
+console.error = () => {};
+console.warn = () => {};
+console.info = () => {};
+console.debug = () => {};
+
+// Set environment to ensure logger suppression
+process.env.MCP_MODE = 'stdio';
+process.env.DISABLE_CONSOLE_OUTPUT = 'true';
+process.env.LOG_LEVEL = 'error';
+
+// Import and run the server
+import { N8NDocumentationMCPServer } from './server-update';
+
+async function main() {
+  try {
+    const server = new N8NDocumentationMCPServer();
+    await server.run();
+  } catch (error) {
+    // In case of fatal error, output to stderr only
+    originalConsoleError('Fatal error:', error);
+    process.exit(1);
+  }
+}
+
+// Handle uncaught errors silently
+process.on('uncaughtException', (error) => {
+  originalConsoleError('Uncaught exception:', error);
+  process.exit(1);
+});
+
+process.on('unhandledRejection', (reason) => {
+  originalConsoleError('Unhandled rejection:', reason);
+  process.exit(1);
+});
+
+main();