It seems than rpm now consider two packages shipping the same directory as a conflict:

Installation failed: file /etc/nagios from install of nrpe-2.13-2.mga3.x86_64 conflicts with file from package nagios-1:3.4.1-7.mga3.x86_64

My options are:
- make nrpe package conflict with nagios package
- make nrpe package ship a file under /etc/nagios without shipping the directory
- make nrpe package install its configuration file elsewhere
--
BOFH excuse #258:

That's easy to fix, but I can't be bothered.

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