You must use a merge file. All possible merge-files you find here:

http://xdoclet.sourceforge.net/xdoclet/ant/xdoclet/modules/jboss/ejb/JBossSubTask.html

the very tricky thing is, that you must build the package-structure and store 
the file in the right package. Here is my structure:

Source-code:
src/main/java/ch/imis/ishop/ejbbackend/article/ejb

The merge-directory:
src/xdoclet

now you must build inside the merge-dir the package-structure like this:
src/xdoclet/ch/imis/ishop/ejbbackend/article/ejb

and store the merge-file there.

In the ant-task you must specify the merge-dir:
<ant:ejbdoclet 
                        addedTags=""
                        excludedTags=""
                        destDir=""
                        verbose=""
                        mergedir="/src/xdoclet">

my merge-file-name:
jbosscmp-jdbc-Article.xml
Article stands for the ejb-class-name

Another hint:
A merge-file defines a part of the whole target-xml-file, so you must specify 
the whole part and can't specify only the things you need additional to the 
specified tags inside the class-file. Will also mean the xdoclet-tags inside 
the class will not be considered for the part of the merge-file


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