Recover from wrong Wi-Fi password on Arduino Yún
The simplest option is to provide a serial console interface which will either give full access to the OS (pipe through Console) or a menu driven interface that sends instructions to the main chip (through Bridge).

The user would then connect to the USB interface and use a terminal program to access the configuration in whatever way you have chosen.  This could either be via options within your installed sketch, or by uploading a special sketch through the USB connection.