It seems the cat protector project documentation has a small gap. There is just a hint that you have to use some scripts to prepare the SD card to play the audio files, but no details about this.
To use the scripts you need some knowledge how to use a command line interface on your operating system. The scripts are very simple to use on Linux and Mac OS X, but on Windows it is very tricky. I strongly advice you to use either Linux or Mac OS X. If you are working on Windows, just use a free virtual machine application and install a Linux (I suggest Ubuntu) or a Linux live CD where you don’t have to install anything.
Why? …. Why … that … complicated
The used microcontroller is not very fast, if the software on the microcontroller also has to deal with a complicated filesystem, no sequential blocks and other obstacles, changes are small to produce sound output in a good quality. Therefore I prepare the samples in a very simple format and instead of a complicated file system, I just store the blocks with the audio data sequentially onto the SD card.