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How do you organise home with a script?

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http://www.unix.com – Hi, I am helping my dad with his computer and he has the messiest folder organisation imaginable. Would it be possible to create a script which moves all images not in the Pictures folder to pictures, all documents not in Documents to Documents, videos to Videos etc? But of course ignoring hidden directories as that would ruin settings! From the home directory root because he sometimes saves files in the home root. And in folders in the Desktop. Would it ignore links too? Like if I put links on his Desktop to Documents, Pictures etc I hope it wouldn't go through those because that would (HowTos)