Anders,
Removing the absolute paths is currently an enhancement request. As a workaround, what we recommend is that development teams only place the .xdoclet file into source control and then have each developer simply open the XDoclet settings panel and select OK in ourder to build a custom xdoclet-build.xml file for their configuration.
There’s a discussion of what files should go into version control in this thread, if you’re interested:
https://www.genuitec.com/forums/topic/source-control/#post-210942