As a preview of a feature available in the nighty builds, a large change was made to how KiCad stores and loads settings that not only fixes a few headaches with the old system but lays the groundwork for more customization in KiCad such as color themes. This was thanks to the work of Jon Evans in MR#68
Since KiCad 4.0, work has been progressing to overhaul all the various project file formats that among many benefits, make them far more human friendly, easier to parse and allow easier addition of new features.