lib/deploy: Split /etc merge into two stages
lib/deploy: Split /etc merge into two stages

For staged deploy, we want to pay the cost of creating copies from
`/usr/etc` → `/etc` at stage time, since it can be expensive.  (We
want to minimize time spent during shutdown).

Split it up into two functions; the logic is also simply clearer.

Closes: #1514
Approved by: jlebon

GNOME/ostree,GNOME/ostree,GNOME/ostree,GNOME/ostree,GNOME/ostree