Move Jia settings

This moves Jia settings to a `conf` directory like Kronos and Metis have.

The Metis `runserver` used to override `debug` and `port` in the settings file even if they were not specified by the user on the command line, so the changes to that file fix that.
@usmanm The default port is specified in the default settings file if not a user supplied settings file. If you specify a default on the command line then it will always override any settings file.