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It should be there, make sure you are booting up from the SD. An easy way to know is to check this is during the booting process if the Grub menu is red you then you are not booting up from the SD, it should be blue. Another way to upload the blink sketch, remove the USB and the power and then plug the power cord again if the sketch resumes the blinking its booting up correctly. Also the files for node and python are under /usr/lib. I hope you find this useful.