remove file options not matching any setting

The old configuration manipulation functions always created an empty
file and dumped the settings into this file. Therefore the configuration
file always exactly matched the written settings.

The current augeas based implementation does not need to build the
configuration file from scratch and precisely updates only the
configuration options while keeping old file structure.

The current implementation missed the synchronization step which removes
the unused keys. This patches adds the support for it.

Related to #205

Signed-off-by: Jakub Filak <jfilak@redhat.com>