Problem is solved by help from Gunnar from the hibernate team. (https://forum.hibernate.org/viewtopic.php?f=9&t=1029612)
The solution was to copy the commons-codec-1.8.jar to the module folde of apache lucene in my jboss installation (JBOSS_HOME/modules/org/apache/lucene/3.6.2) and make an entry in the module.xml.
After that the phoneticfilterfactory, especially the colognephonetic, was found and my indexing is working.
Thanks to everyone who has helped.