Split out from https://fedorahosted.org/freeipa/ticket/3566
Currently IPA's default permissions merge user changes and changes from IPA upgrades incorrectly. Since we're aiming for more configurability we need to address this problem.
Metadata Update from @pviktori:
- Issue assigned to pviktori
- Issue set to the milestone: FreeIPA 4.0 - 2014/02
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