Why it shows "You are opening the application 'Xcode' for the first time? I am running XCode v.5.1 in my Mountain Lion, I don't know why, but I'm getting this message after a successful start of Mac computer. I was already using this version of XCode before and now suddenly it's showing me this message? What's wrong? It is something that Apple forgets its my first run?
If you're not able to set the quarantine status on the app, then it will forever have that status and will prompt you. You can manually remove quarantine from the app with…

xattr -d com.apple.quarantine /Applications/Xcode.app