Stop if `output_directory` is non-empty

[PGijsbers]

Running GAMA twice with the same output_directory is currently valid, but the result will be that all the log files are concatenated, which is nonsensical and also leads to errors when parsing. By default GAMA should stop if it detects the output directory is non-empty. Maybe we can add another parameter to specify to overwrite existing files (probably won't give an option to support the current append behavior as we shouldn't really want to support parsing multiple file formats).