Fix MCP stdio protocol violation during startup

The MCP protocol requires the client to send the first message. Writing
to stdout before the client's initialization request breaks the protocol
handshake, causing 'BrokenResourceError' in clients like langchain-mcp-adapters.

Root cause: Transport was created AFTER config/feature flags initialization,
so logger.* calls during startup wrote directly to stdout (bypassing buffering)
or called sendLog() which also wrote to stdout without checking isInitialized.

Fixes:
1. Move FilteredStdioServerTransport creation before config loading
2. Buffer sendLog() messages when isInitialized is false
3. Guard sendProgress/sendCustomNotification when not initialized

Fixes #issue-reported-by-ever1022

Author: wonderwhy-er

src/custom-stdio.ts

@@ -277,13 +277,25 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
 
   /**
    * Public method to send log notifications from anywhere in the application
+   * Now properly buffers messages before MCP initialization to avoid breaking stdio protocol
    */
   public sendLog(level: "emergency" | "alert" | "critical" | "error" | "warning" | "notice" | "info" | "debug", message: string, data?: any) {
     // Skip if notifications are disabled (e.g., for Cline)
     if (this.disableNotifications) {
       return;
     }
 
+    // Buffer messages before initialization to avoid breaking MCP protocol
+    // MCP requires client to send first message - server cannot write to stdout before that
+    if (!this.isInitialized) {
+      this.messageBuffer.push({
+        level,
+        args: [data ? { message, ...data } : message],
+        timestamp: Date.now()
+      });
+      return;
+    }
+    
     try {
       const notification: LogNotification = {
         jsonrpc: "2.0",
@@ -315,6 +327,11 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
    * Send a progress notification (useful for long-running operations)
    */
   public sendProgress(token: string, value: number, total?: number) {
+    // Don't send progress before initialization - would break MCP protocol
+    if (!this.isInitialized) {
+      return;
+    }
+    
     try {
       const notification = {
         jsonrpc: "2.0" as const,
@@ -346,6 +363,11 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
    * Send a custom notification with any method name
    */
   public sendCustomNotification(method: string, params: any) {
+    // Don't send custom notifications before initialization - would break MCP protocol
+    if (!this.isInitialized) {
+      return;
+    }
+    
     try {
       const notification = {
         jsonrpc: "2.0" as const,

src/index.ts

@@ -39,6 +39,13 @@ async function runServer() {
     // Set global flag for onboarding control
     (global as any).disableOnboarding = DISABLE_ONBOARDING;
 
+    // Create transport FIRST so all logging gets properly buffered
+    // This must happen before any code that might use logger.*
+    const transport = new FilteredStdioServerTransport();
+    
+    // Export transport for use throughout the application
+    global.mcpTransport = transport;
+
       try {
           deferLog('info', 'Loading configuration...');
           await configManager.loadConfig();
@@ -56,10 +63,6 @@ async function runServer() {
           // Continue anyway - we'll use an in-memory config
       }
 
-    const transport = new FilteredStdioServerTransport();
-    
-    // Export transport for use throughout the application
-    global.mcpTransport = transport;
     // Handle uncaught exceptions
     process.on('uncaughtException', async (error) => {
       const errorMessage = error instanceof Error ? error.message : String(error);