Fix folder colors not saving after project.godot is modified externally

[KoBeWi]

1. Open a project
2. Open project.godot in text editor, modify and save it
3. When external modification prompt appears in Godot editor, reload the file
4. Assign folder colors
5. The colors won't be saved until you restart the editor, meaning all your new colors are lost

This PR updates Dictionary reference when project settings are changed, so it can be saved properly.

[akien-mga]

Thanks!