This might help: http://www.espruino.com/Saving
An image of what's currently in RAM is compressed and written to flash. It looks like right now it's not getting compressed enough to fit in to the 2k reserved for saved code (there's more flash used outside of this for the Espruino firmware).
Best bet for the moment is to use the IDE's 'save to flash' method, which writes a textual version if your code into flash (rather than trying to image RAM)
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