Amir,
Sorry that you are seeing this issue.
1. Did you migrate the project after importing to MyEclipse for Spring 2014? Did you see any errors during migration?
2.Can you please let us know what exact error do you see on the xml heading? Check the Problems view for the error. If possible send us the project to help us replicate the issue at our end. Please send us the project before migration to MyEclipse 2014.
3. I have already raised an enhancement request to add support for hibernate mapping during scaffolding. I suggest you cross post to development forums for help about the issues you are seeing when adding the Hibernate mapping manually to the scaffolded project.