1: This is fine - if you upload code to Flash on Espruino (as long as you don't turn on minification) it'll all be inside the board, including comments, and can be read straight out using the IDE.
2: You can't do this directly on Espruino without the flash drive (although you can do it just by going to espruino.com/ide and clicking the Storage button). In that case I'd suggest making a webpage that'll handle the data collection though. Full code of doing exactly that is at http://www.espruino.com/Data+Collection#automatically-recovering-data
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