EJB3.1 introduces a "inherited" attribute for application-exception element in ejb-jar.xml:

<xsd:complexType name="application-exceptionType">
<xsd:annotation>
<xsd:documentation>

The application-exceptionType declares an application
exception. The declaration consists of:

• the exception class. When the container receives
  an exception of this type, it is required to
  forward this exception as an applcation exception
  to the client regardless of whether it is a checked
  or unchecked exception.
• an optional rollback element. If this element is
  set to true, the container must rollback the current
  transaction before forwarding the exception to the
  client. If not specified, it defaults to false.
• an optional inherited element. If this element is
  set to true, subclasses of the exception class type
  are also automatically considered application
  exceptions (unless overriden at a lower level).
  If set to false, only the exception class type is
  considered an application-exception, not its
  exception subclasses. If not specified, this
  value defaults to true.

</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="exception-class"
type="javaee:fully-qualified-classType"/>
<xsd:element name="rollback"
type="javaee:true-falseType"
minOccurs="0"/>
<xsd:element name="inherited"
type="javaee:true-falseType"
minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>

The metadata schema mapping class should support this new attribute.