This switches to a secure FS implementation in most places, except for
where we can not make changes at this moment because it would break
behavior.

Not handled in this commit:

- Allowing the root for `manifestgen` packages to be configured.
- Allowing the user to define a working root while building locally.
- Defaulting to the secure FS implementation in
  `kustomization.MakeDefaultOptions`. Problem here is that constructing
  the secure FS could result in an error, which we can not surface
  without signature changes to the constructor func.

Signed-off-by: Hidde Beydals <hello@hidde.co>