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There are many files and folders that are created by applications but they are not showing up on my home folder. Also, searching for them in the Dash does not bring them up either. Can I bring them up through the terminal? Or are they locked somehow?

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What specific folders/files? Did you Ctrl+H to show the hidden ones? – wojox May 30 '12 at 23:40
There are a lot of configuration files created in the directory "/etc". They are there because they are not user-specific, but still made to edited by an administrator, using sudo. – Marty Fried May 30 '12 at 23:45

To show hidden files with nautilus press CTRL + H To list all files in a Terminal type

ls -a
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ls -a in terminal works. You can also push ctrl+h in nautilus or dolphin (file browsers) to show hidden files. No, they aren't locked, they are just hidden by default because their names start with a ".".

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You can find files from a terminal with:

$ find -name <filename>
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