/etc/apt/apt.conf.d/ priority - overrule configuration file?
Source: http://debian-handbook.info/browse/wheezy/sect.apt-get.html
Directories ending in .d
Directories with a .d suffix are used more and more often. Each directory represents a configuration file which is split over multiple files. In this sense, all of the files in /etc/apt/apt.conf.d/ are instructions for the configuration of APT. APT includes them in alphabetical order, so that the last ones can modify a configuration element defined in one of the first ones.
For example 60unattended-upgrades should overrule 50unattended-upgrades.