Fix unchecked memory access for files
This PR takes care of two problems:
- It uses `Memory::(read|write)_bytes` to guarantee that memory accesses are checked (Fixes: https://github.com/rust-lang/miri/issues/1007)
- It removes the `(get|remove)_handle_and` methods which were a little bit cumbersome to use. In particular `remove_handle_and`, because we were using it to avoid borrowing issues before the `Evaluator::memory` field was public.
@RalfJung @oli-obk