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/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();