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System files and directories generally belong to root. When logged in as root it is easy to mistakenly delete or modify them in such a way as to require a complete reinstallation of the system.
When logged in as a user that user can only modify files he owns so he can't trash the system.
An other tip is to log out almost directly after you done your root-thing. Otherwise you will end up with lots of files and directories that you cannot delete o write to when you are logged in as a normal user.
I understand that one might think that is would be handy to always be root. But believe me. Some guys really regret that mistake when they have to install everything from the beginning again.
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