* Issue #36: a None object was dereferenced in the user's configuration panel. If statement is added to avoid the error.
* Issue #36: Do not create default configuration files. We prefer to let the files empty until the user click on 'apply' in the configuration panel.
* Issue #36: Avoid to output empty values in the configuration file, because the Config::Simple API cannot support this particular case.
* Issue #36: replace 'input.directory' by 'input.project directory' because these two internal variables represent the same directory and are redundant.