How do you remove the "@" from directory entries (extended permissions)

I had a CodeIgniter project that I was creating on my MacBookPro, and then uploaded it to my Mac to sync.
Now, when I go to that project, it won't run in my XAMPP server...giving a Forbidden message. I went to the terminal to do a typical chmod -R on the top directory. Then, looking at an ls for that project I get this "@" at the end of every directory. I understand that this has to do with "extended" permissions?
When I do an xattr -l on the folder (directory) I get this:
kkmac:application kkathman$ xattr -l controllers
com.apple.quarantine: 0000;4d48e195;Firefox.app;|org.mozilla.firefox
kkmac:application kkathman$
Where did the extra set of permissions come from, and how do I get rid of them?
As an incidental issue, I DID run Onyx, as I do once a month, to "fix" permissions. Did this mess everything up?
Thanks,
Korky

Update: This is a weird MacBookPro to MAC issue, that possibly needs to be looked at.
I can reproduce this every time. What I did was download CodeIgniter and unzip it. Rename it if you want, but do nothing else.
Now, TRANSFER that directory tree to a MacBookPro. Then, make a couple of changes to some files.
Now, upload the directory tree BACK to the Mac. I deleted the old tree on the Mac and then put the one from my Laptop back there.
Try to execute. It absolutely won't. It will report "Forbidden" every time. However, go back to the ORIGINAL CodeIgniter base, and you'll find you can load that and run it just fine. So, this copying down and up, has some oddities in it!

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