fix: STDIO transport stdout flush and MCP notification handling

- Wait for stdout.write callback before process.exit in STDIO transport
  to prevent truncation of large responses (e.g. grafana tools/list)
- Handle MCP notification methods (notifications/initialized, etc.) in
  router instead of returning "Method not found" error
- Use -p shorthand in config claude output

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/mcpd/src/services/transport/stdio-client.ts

@@ -61,9 +61,10 @@ proc.stdout.on('data', d => {
       const msg = JSON.parse(line);
       if (msg.id === 2) {
         responded = true;
-        process.stdout.write(JSON.stringify(msg));
-        proc.kill();
-        process.exit(0);
+        process.stdout.write(JSON.stringify(msg), () => {
+          proc.kill();
+          process.exit(0);
+        });
       }
     } catch {}
   }