I don't want to create a new thread, so let me continue posting here 
Here is another thing I found, it related with ROO 1.2.1 version:
ROO generates a database table class and some aspect files. By default it generates for ID column code in *_Roo_Jpa_Entity.aj like
Code:
@Id
@GeneratedValue(strategy = GenerationType.AUTO)
@Column(name = "id")
private Long Favorite.id;
If I move this code to the class file (just to change GenerationType.AUTO to GenerationType.IDENTITY), Roo:
1. removes this annotations only from original *_Roo_Jpa_Entity.aj
2. creates *_Roo_JavaBean.aj and writes there getId() and setId() methods
But, both methods still exists in *_Roo_Jpa_Entity.aj! So we have an error. To fix it I have to move both methods to the class, where an annotation has been moved.
And if I later edit entity class file and remove from there getId() and setId() methods, Roo adds boths methods to *_Roo_Jpa_Entity.aj and also creates *_Roo_JavaBean.aj. SO no way just to move annotation, I have to move methods too.
In Roo 1.1.5 version of STS 2.7.2 this problem didn't exists. Think it is an issue too..