If there are items you do not want to back up using Time Machine, go to System Preferences, Time Machine and click on the Options button. You can add folders and files. Remember that anything you add here will not get restored if your hard drive fails.
Related: Using Time Machine to archive old files?, time machine problem, This Mac & All My Files Difference ?, Set Applications To Auto Startup At Login, Are iTunes files really deleted if deleted in iTunes?.
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