ref #9: added confirmation dialogs

Removed the "Ask confirmation" setting. 
Overwrite is unchecked by default. 
If Overwrite is selected the output files are overwritten. 
If Overwrite is not selected and the output file does not exist or the
output directory is empty, output files are just written.
If Overwrite is not selected and the output file exists or the output
directory is not empty, a confirmation dialog pops up.
Still missing Unit tests