Multiple copies of songs. How do I change my settings?

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Ok I'm having a serious issue. I have multiple copies of songs in Itunes. So I ran a duplicate killer program to get rid of them from my my music folder. Good. Then went thru Itunes and deleted duplicates. Good. I think I also ran a program to rename/organize. SO - here's the issue: Itunes shows a lot of songs have the ! exclamation to show they've moved. Can I somehow clean out my library and start over without losing my purchased stuff? Most of my music is from my own collection - mp3 format, in my my music folder. How should I have the settings so that it automatically puts new songs into Itunes so I don't have to import everything again and end up with multiples again? And if I delete all the files out of Itunes, will it still keep my purchased music. It's a mess and I need help... and apple doesn't make it easy to get help. I can't even figure out how to update my email address on this stupid forums page - my new email is [email protected]
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Under Security & Privacy under System Preferences, check to see what settings you have for "Allow Applications downloaded from..." to select your safest settings. I have mine checked for App Store and Identified developers. You can change it to "Anywhere" to be able to access anything. You should be able to install even with these settings: you'll just have to authenticate with an admin password.
Clinton