See https://bugs.gentoo.org/show_bug.cgi?id=438790 for details, but essentially, polkit-kde-kcmmodules is editing files in /usr, but those files should be static and user changes should be going into /etc/polkit-1/rules.d/. Right now, this is messing up the directory structure and often leads to weird issues when debugging polkit problems (from KDE touching other packages' .policy files), and user settings are frequently overwritten on upgrade. Also, polkit allows /usr to be mounted RO, and this configuration prevents that. Reproducible: Always
Reassigning to the kcm_auth component
I am raising the severity, as current behavior is rather useless - user looses all of his setup on package upgrades...