After the XcodeGhost problem appeared, I checked my version of Xcode (6.4) and discovered that the digital signature didn't match. There was some problem. Was it caused by the XcodeGhost hack? Was it something worse? Or maybe just something benign.
To check, I used the md5deep program that's often used for forensic analysis. I tried to find a friend with a working version but they had bad versions too. There is plenty of corruption going around.
Here are the md5deep results from my version Xcode. If you can help me flag the problems, let me know.
To compare with your version, you can use this command:
md5deep -r -X xcode-md5deep-2015-09-23-12-30.txt /Applications/Xcode.app