What do you mean by "Ride don't make correctly a new CircleOS application" ?
If the installlation is correct, the necessary files (including FAT.elf) for creating and building Circle applications are located in "{Ride}/lib/ARM/CircleOS", and "{Ride}/lib/ARM/CircleOS/Circle_App".
Concerning the directory structure, I suppose that you are talking about the CircleOS sources files. Effectively, in order to manage the different new platforms (EvoPrimer STM32 and STM8 target boards), we were obliged to separate common and specifics files.