Xcode messing up Desktop Folder icons

When I run Xcode 6.1.1 on Mac OS 10.9.5 I get the message:

Install additional required components?

I choose Install. Fine it installs.

But many of my desktop folder icons have become generic file icons!

I have tried to fix this by deleting the dock icons and system icons cashes using Onyx but this did not work.

The only fix is to reinstall OS X but now Xcode wants to reinstall components.

So what is the fix for this?