Updater: fix the loci-common.jar issue

The commit fce7ba31(Updater: make 'install them all' non-conflicts) was
incomplete: it not only turned the conflict into a notice, it also
reverted marking the automatic installations.

That led to loci-common.jar being reported as an automatic install,
but without installing it automatically.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Updater: avoid deprecated Conflict constructor

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>