While upgrading the XWiki Enterprise Manager - UI from 3.5.1 to 5.0M2, after having properly repair 3.5.1, all package that have a change in their names, like administration vs administration-ui, are not merged.
These package are shown as applying INSTALL and not applying UPGRADE.
List of affected package:
administration => administration-ui
appwithinminutes => appwithinminutes-ui
blog => blog-ui
invitation => invitation-ui
livetable => livetable-ui
panels => panels-ui
statistics => statistics-ui