JBoss Tools 4.3.0.Beta2 and newer includes a new feature (always on) that explodes jars in a deployment if the server adaptor supports it. WildFly does.
This means that you now have exploded jars inside an exploded deployment which apparently is a problem for db_bootstrap because it cannot find the classes specified in its configuration.
While the configuration below works with JBoss Tool 4.3.0.Beta1, it breaks in JBoss Tool 4.3.0.Beta2 and newer with a ClassNotFoundException for com.example.Bootstrapper. The difference being that in Beta2, the class is located in some com.example*.jar while in Beta2, the class is exploded in the directory com.example*.jar/com.example. It also fails if the filter-on-name attribute is removed.
<scan name="Myname" filename="MyEar.ear" filter-on-name="com.example*.jar">
<class name="operation" classname="com.example.Bootstrapper" />
</scan>
The JBoss Tools 4.3.0.Beta2 feature: https://issues.jboss.org/browse/JBIDE-15250