What device are you using? Bangle.js, or something else?
Honestly I'm not sure you're going to have much luck trying to force the Web IDE in to uploading a file - the file upload there is designed to use Storage.
The best solution is:
Base 64 Flash Write
And you should be sorted!
If you want to automate it, it should be reasonably easy to mash the File Converter code together with the Web Bluetooth example at http://www.espruino.com/Web+Bluetooth to make a website that will upload directly
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