The ps3keys file contains the master key set for the system, while the scetool/data/ is specifically for the scetool utility, which is used to encrypt and decrypt SELF and PKG files. The wiki also confirms that keyfiles should be placed in ~/.ps3 or %userprofile%\ps3keys .
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For example, on the ConsoleMods Wiki, you can find the official MD5 hash for a firmware PUP file. You would then check the hash of your downloaded .PUP file against it.
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| File Prefix | Key Type / Purpose | | :--- | :--- | | | System keys for the lowest-level system "hypervisors" (root keys for system control). | | app | Used for signing and verifying application executables (EBOOTs). | | iso | Keys for handling decrypted ISO disc images. | | pkg | Keys for decrypting and installing PKG package files (DLC, updates). | | np (or npdrm) | Keys for dealing with NPDRM (Network Product DRM) protected content. | | ldr | Loader keys used in the early stages of booting content. | The RPCS3 emulator has revolutionized PS3 gaming
You should back these up from your own PS3's exdata folder using a tool like multiMAN or Apollo Save Tool .