Can I talk to the computer that I am plugged into over the USB connection?

Thanks! Glad you're finding it useful!

it's mac I develop on and linux it'll be installed on

Awesome, then it sounds like USB HID is the really easy fix.

If you do have a process running then yes, you could use MQTT. It might be overkill though...

For USB serial, take a look at http://www.espruino.com/Interfacing

You might find it's easier to just use Espruino's REPL and post raw JS commands to it...

But if not, you can use Serial1.setConsole to move the REPL out of the way so you get full access to the USB serial port with USB.write and USB.on('data', ...)