Nowadays it is very common to have config files in three different places:
/usr/share/app. These are the config files that come with the distro package. Different packages can provide config droplets to other packages. They should never be changed by the user, so that package upgrades can work without conflicts.
/etc/app. These are the machine-installation-specific config files. They win over 1, so any customization for your local installation goes in here.
~/.config/app. These are user-specific config files. They win over 1 and 2.
Nowadays it is very common to have config files in three different places:
/usr/share/app. These are the config files that come with the distro package. Different packages can provide config droplets to other packages. They should never be changed by the user, so that package upgrades can work without conflicts./etc/app. These are the machine-installation-specific config files. They win over 1, so any customization for your local installation goes in here.~/.config/app. These are user-specific config files. They win over 1 and 2.