API for upload code into device?

Of course you can, there is nothing special in the IDE. You have Espruino interpreter console on the serial port so you can do everything. Just send the code directly 'as is' to serial port and it gets executed immediately (so you may start with sending reset() if you want to start from scratch) or you can execute code that will write it to storage and reboot

there is also espruino command https://github.com/espruino/EspruinoTool­s that may be easier for you