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Files are not showing up on the Thumbdrive or eeePC correctly

Here’s what’s going on: a couple of students copied their thumbdrive (the entire directory) on to the hard drive.
So, when students went to open the D: drive, the computer went to open the D: folder on the hard drive, and never
recognized the new thumbdrive. So students need to be coached to be careful to only copy files, not the whole thumbdrive.
OR, to simplify things, have all files ONLY on the thumbdrive.