kustomize: use FS from fluxcd/pkg

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>

pkg/manifestgen/kustomization/options.go

@@ -25,6 +25,8 @@ type Options struct {
 }
 
 func MakeDefaultOptions() Options {
+	// TODO(hidde): switch MakeFsOnDisk to MakeFsOnDiskSecureBuild when we
+	//  break API.
 	return Options{
 		FileSystem: filesys.MakeFsOnDisk(),
 		BaseDir:    "",