PUP-3341 - make apply work again, even when facing an ENC environment

This concludes the partial fix for PUP-3258 in #3118 (on which this branch is based).

It enforces the manipulated apply environment again, which is the right way I feel.

We might discuss whether it would be cleaner to replace the current way of
 * take `:current_environment`
 * override `:manifest` to what was supplied on the commandline
 * lookup node
 * force overridden environment onto node

to a more cordial

 * lookup node
 * override `:manifest` in its environment
 * force overridden environment onto node