Fix #199 Auto add directories for rpm.

* Permanent fix for #199. Provides a `--rpm-auto-add-directories` option to add directories
   not part of the filesystem package.
* The listing from filesystem package is in `templates/rpm/filesystem_list`.
* The filesystem package is not updated frequently so should not be a problem maintaining
   the list (Last update was in 2011).
* prefix handing for `config_files` and `directories` moved from the template to the library.