Loader: Updated read methods to be const

- Required "file" handle to be made local and explicitly opened/closed as needed
Marked AppLoader_ELF, AppLoader_NCCH, and Archive_RomFS classes as "final"
Marked AppLoader_ELF, AppLoader_NCCH, and Archive_RomFS virtual functions as "override".
Archive: Added Init/Shutdown methods to reset kernel archive state.