Answer
By tying SIO_2 High and SIO_13 to GND the module will automatically start up in OTA mode without any user interaction. Once an application is loaded, the $autorun$ code will start running upon the next reset because SIO_13 is tied to GND. It is important that a way to delete the $autorun$ file to re-enter OTA mode to load a new file is included. This method will either be a command that is sent over BLE that triggers the EraseFileSystem() function or will need a GPIO that triggers this function.