Commit 1829fb61 ("manifest: Fix crash on startup when trying to clean up
unused files (#5840)") changed the config layer stored in manifests
from a pointer to a value. This was done in order to avoid potential
nil pointer dereferences after it is deserialized from JSON in the
event that the field is missing.
This changes the Layers slice to also be stored by value. This enables
consistency in handling across the two objects.
