After I have upgraded both Xcode (to 6.0.1) and OS X Server (to 3.2.1) I can\'t figure out how to add certificates for the provisioning profiles so the Xcode bot can find th
For OX X Server 4.0 and XCode 6.1 is a much easier way:
Open your Project with XCode on the Server add your Developer Account to "Accounts" and download all required provisioning profiles.
Copy your Privisioning Profiles from /Users//Library/MobileDevices/Provisioning Profiles/ into /Library/Developer/XcodeServer/ProvisioningProfiles/
Give read and write access for administrators for the folder /Library/Developer/XcodeServer/ProvisioningProfiles/
Open KeyChaine Access double click on the provisioning profile keys (for example iOS Developer: XY) and allow access for all apps.
Done.