Add an "output-dir" configuration option

[Konamiman]

Add an output-dir option to the configuration file.

This allows to specify the base output directory for the generated prefixed files in the configuration file, the same way as the command line option of the same name already does. If both are present, the command line option takes precedence.

[Konamiman]

@theofidry I've pushed a commit with the changes you suggested.