some comments about pandora code

[LilySnow]

1. Please replace system() with one of subprocess functions, e.g. subprocess.check_call(), subprocess.check_output().
2. Do not change directories in your code. (only use it for quick and dirty code).

[DarioMarzella]

Additional comments on code quality and logic following:
3. PANDORA.Pandora object takes now the "output_dir" argument. This is not very logical. It should be moved to PANDORA.model.