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If it were possible to detect changes in a file using a web file API then we could make some changes and it'd be possible for you to use the Web IDE as just a terminal/upload tool for whatever editor you wanted - but it seems it isn't right now
With which browser did you test this behavior? I think I used an application a few years ago which detected changes in a textfile on disk and it only worked w/ chrome.
Yes - you just install the Espruino command-line app from https://www.npmjs.com/package/espruino
Worth noting that on Windows it can be tricky trying to get Bluetooth Low Energy comms to work nicely from Node.js. It's one of the reasons the Web IDE really helps.
If it were possible to detect changes in a file using a web file API then we could make some changes and it'd be possible for you to use the Web IDE as just a terminal/upload tool for whatever editor you wanted - but it seems it isn't right now