Duplicate applications list

I recently got a new iMac. I transferred everything from my old iMac via ethernet during the startup process.
Now, when I tried to email a link, using the "Share" function in Safari, it opens a second Mail on the dock. When I checked that Mail with "show in finder," it showed that I have a folder in Applications called "copy to Applications," which contains a duplicate list of my applications.
But if I select iMessage from the share list, it goes to the regular iMessage in the regular Applications folder.
In both iMessage and Twitter, if I click on a link, and I already have Safari open, the link opens in that Safari (from the Applications folder). But, if Safari is not open, they will open a second Safari on the dock from the "copy to Applications" folder.
I found on my old iMac (the one I transferred from), there is also a "copy to Applications" folder in Applications, but it is an alias, pointing to the actual Applications folder. Not an alias in the new iMac.
I tried putting the "copy to…." in the trash, but then those links result in a "can't find…" warning (or something like that). So I put it back.
What to do to stop things from looking for this "copy to…" folder?
Thanks.

Hi, I think you need to trash that copy to folder, then rebuild the Launch db...
Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions...
Reset Launch Services...
http://www.thexlab.com/faqs/resetlaunchservices.html#Anchor-Reset-47857
Reboot.
PS. Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive.

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