Hi Sergei and Todor,
If you are going to execute Maven from the parent then you should specify the full-path to your directory filesets. If you are going to execute Maven from the child module you can specify either relative or full-path to your directory fileset, like this:
<!-- Copy Unix shell scripts, make sure that line ending is LF and an execution permission is set -->
<fileMode>0744</fileMode><!-- rwxr..r.. -->
You see how I have specified the complete path to the directory in my fileset?
In my opnion the maven-assembly should NOT be changed, but I provide a patch if anyone wants to change it. I just add the basedir property to your fileset directory property. In this case you have to specify the directory as relative path.