fix: integrate centralized logger across services and hooks for improved logging consistency

src/servers/mcp-server.ts

@@ -6,11 +6,16 @@
  * Maintains MCP protocol handling and tool schemas
  */
 
-// CRITICAL: Redirect console.log to stderr BEFORE any imports
+// Import logger first
+import { logger } from '../utils/logger.js';
+
+// CRITICAL: Redirect console to stderr BEFORE other imports
 // MCP uses stdio transport where stdout is reserved for JSON-RPC protocol messages.
 // Any logs to stdout break the protocol (Claude Desktop parses "[2025..." as JSON array).
-const _originalConsoleLog = console.log;
-console.log = (...args: any[]) => console.error(...args);
+const _originalLog = console['log'];
+console['log'] = (...args: any[]) => {
+  logger.error('CONSOLE', 'Intercepted console output (MCP protocol protection)', undefined, { args });
+};
 
 import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
@@ -18,7 +23,6 @@ import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js';
-import { logger } from '../utils/logger.js';
 import { getWorkerPort, getWorkerHost } from '../shared/worker-utils.js';
 
 /**