Bug 25078: Keep atomic updates in "atomicupdate" dir

Bug 25078: Keep atomic updates in "atomicupdate" dir

The atomicupdate directory will contain all the atomic update files (old
and new version).
That will ease job for the RM and RMaints, no file (except skeletons)
must be in this directory before push.

This patch also fixes an inconsistency we had: the atomic update was run
before the other db revs on the UI but after when the CLI script was
used.

Now we make sure that the CLI does not deal with the atomic update files
when called from the installer (UI)

Signed-off-by: Kyle M Hall <kyle@bywatersolutions.com>
Signed-off-by: Jonathan Druart <jonathan.druart@bugs.koha-community.org>