In a frugal installation of Puppy the linux directory structure is contain in a read only SFS file (also known as PupSfs) . It contains the original configuration of the Puppy version and RootFS, any changes are stored in a SaveFile.
For example, the BaseSFS file in Puppy 5.28 is lupu_528.sfs.
Only files stored in the /mnt directory will be saved outside the SaveFile. For example, /mnt/home and /mnt/sda2 are the root directories of the boot partition and sda2 partition respectively.