Bug 20256: (QA follow-up) Make atomicupdate idempotent

Bug 20256: (QA follow-up) Make atomicupdate idempotent

Without this patch, running the atomicupdate twice crashes on patrons
with edit_items permissions:

C4::Installer::run_atomic_updates(): DBI Exception: DBD::mysql::db do failed: Duplicate entry '19-9-edit_any_item' for key 'PRIMARY' at /kohadevbox/koha/installer/data/mysql/updatedatabase.pl line 24303
DEV atomic update /kohadevbox/koha/installer/data/mysql/atomicupdate/bug_20256.perl  [14:26:41]
ERROR - C4::Installer::run_atomic_updates(): DBI Exception: DBD::mysql::db do failed: Duplicate entry '19-9-edit_any_item' for key 'PRIMARY' at /kohadevbox/koha/installer/data/mysql/updatedatabase.pl line 24303

It also aligns this 3yro script with the new structure we've been using.

Signed-off-by: Tomas Cohen Arazi <tomascohen@theke.io>