Bug 32350: Use array_minus and ignore nesting

Bug 32350: Use array_minus and ignore nesting

Note: Test will be extended in follow-up. This fixes the
module_bit hash to follow the FK path from user_permissions
to permissions to userflags. One step was missed in the
existing test, although it did not fail. The change here
revealed that now.

Test plan:
Run t/db_dependent/TestBuilder.t

Signed-off-by: Marcel de Rooy <m.de.rooy@rijksmuseum.nl>
Signed-off-by: Martin Renvoize <martin.renvoize@ptfs-europe.com>
Signed-off-by: Tomas Cohen Arazi <tomascohen@theke.io>