[ARCHETYPE-649] work around warning 'Don't override file...'

[WolfgangHG]

This pull request tries to work around a warning "Don't override file ..." or "CP Don't override file..." that appeared after switching from maven archetype plugin 3.1.2 to 3.2.1 - more details and a sample see https://issues.apache.org/jira/browse/ARCHETYPE-649

The warning seems to be caused by fileset declarations in "archetype-metadata.xml": with 3.2.1, the archetype jar file contains entries for all directories, but before there were only entries for the actual files in the zip. I could also verify this difference by analyzing the jar file with WinZip.

I could work around the warning by switching off "IncludeEmptyDirs" in two places in "JarMojo.execute".

My first thought was to pass the paths of the "archetype-metadata.xml" filesets to the second argument of "DefaultFileSet.includeExclude()", but this did not have any effect - but this might also be caused by me using wrong paths;-)

[DISCLAIMER] This is my first pull request to maven, I don't have knowledge of the internals - just trying to workaround an issue that I run into. Maybe the problem is also caused by me misusing the filesets in "archetype-metadata.xml". So please consider this more a start of a discussion that a "I have fixed something" statement ;-). If you have better suggestions to resolve this, please point me to them.