Keep track of manually vs. automatically-installed packages

[KellerFuchs]

Currently, apt considers all packages in packages.txt to have been installed manually.

This makes getting rid of packages installed as dependencies quite annoying, since apt-get autoremove cannot remove anything.

[RyanSquared]

As a note, when we move to Ansible, this can be done - I think - by just adding more items to a list in a YAML file and then using Ansible's apt module to sync state and autoremove, once we get it working.