doc: Discourage use of '-c config' for repogen tool

'--config file' was deprecated in 9561e4cd6185b461646d1910e80bc849b677711d
but not reflected in the documentation, so removing the references to it.

Also fixing a typo where the 'repository' parameter was duplicated

  repogen.exe ... repository <repository_directory>

leaving only <repository_directory> as follows:

  repogen.exe -p <package_directory> <repository_directory>

Change-Id: I547e7fd68b19ef42afdd096572216c8e2261f03a
Reviewed-by: Niels Weber <niels.weber@digia.com>
Reviewed-by: Tim Jenssen <tim.jenssen@digia.com>