Towards https://github.com/denoland/deno/issues/18455
`safe`, `add` and `rem` options are not implemented because there is no
rust crate that provides this functionality (except rust-openssl maybe)
and its just not clear if this API is used widely.
We can make `NodePermissions` rely on interior mutability (which the
`PermissionsContainer` is already doing) in order to not have to clone
everything all the time. This also reduces the chance of an accidental
`borrow` while `borrrow_mut`.
