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The PS Vitas File System is different to the one from the psp and similar if not the same like the one from the PS4.

There are now some additional folders within a folder structure of a application. The frist one sce_sys which is already present in the pkg it self. And then there is sce_pfs placed in the root of the Title_ID folder, and package which will be both created douring the installation and where the last named one will be placed into sce_sys.