subsys: fs: Fix fs_file_t and fs_dir_t usage

With the introduce of VFS the typedef for fs_file_t & fs_dir_t don't
exist anymore so we need to use 'struct fs_dir_t' or 'struct fs_file_t'.
Fix up some places that got missed in the VFS conversion.

Signed-off-by: Kumar Gala <kumar.gala@linaro.org>