The majority of user settings are stored in a config file, which is loaded by the user after the program has started. Current, the format of the config files is XML, and JSON support will likely be added.
Currently, the config files are edited manually, but this is not the long term vision. Config files will be generated by the GUI where the majority, if not all, of options should be available. Manual editing of the config file should only be necessary for special cases or features not yet implemented in the GUI.
This config will also be used by add-on processes concurrently as a way to communicate global settings.