Finaly I used JD-gui to decompile and read the code of the plugin and I managed to do it running 2 times the plugin with the goal hbmtemplate each times using a different template : one for the entity one for the dao.
I found out that it is possible to use a custom exporter by specifying it in exporterclass. maven plugins lack some king of xsd...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>hibernate3-maven-plugin</artifactId>
<version>2.2</version>
<executions>
<execution>
<phase>generate-sources</phase>
<id>genpojo</id>
<goals>
<goal>hbmtemplate</goal>
<goal>hbm2ddl</goal>
</goals>
<configuration>
<components>
<component>
<name>hbmtemplate</name>
<implementation>configuration</implementation>
<outputDirectory>src/main/java</outputDirectory>
</component>
<component>
<name>hbm2ddl</name>
<implementation>configuration</implementation>
<outputDirectory>src/main/resources/sql</outputDirectory>
</component>
</components>
<componentProperties>
<jdk5>true</jdk5>
<format>true</format>
<configurationfile>src/main/resources/hibernate/hibernate.cfg.xml</configurationfile>
<drop>true</drop>
<create>true</create>
<outputfilename>init.sql</outputfilename>
<templatepath>src/main/resources/templateftl</templatepath>
<filepattern>{package-name}/pojogen/{class-name}.java</filepattern>
<template>pojo/Pojo.ftl</template>
</componentProperties>
</configuration>
</execution>
<execution>
<phase>generate-sources</phase>
<id>gendao</id>
<goals>
<goal>hbmtemplate</goal>
</goals>
<configuration>
<components>
<component>
<name>hbmtemplate</name>
<implementation>configuration</implementation>
<outputDirectory>src/main/java</outputDirectory>
</component>
</components>
<componentProperties>
<jdk5>true</jdk5>
<format>true</format>
<configurationfile>src/main/resources/hibernate/hibernate.cfg.xml</configurationfile>
<drop>true</drop>
<create>true</create>
<templatepath>src/main/resources/templateftl</templatepath>
<!-- <exporterclass>com.db.exporter.MyDAOExporter</exporterclass>-->
<filepattern>{package-name}/daogen/{class-name}Dao.java</filepattern>
<template>dao/daohome.ftl</template>
</componentProperties>
</configuration>
</execution>
</executions>
</plugin>