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Ah, it appears that it was installed from source, so the instructions at https://github.com/progrium/dokku/blob/master/docs/upgrading.md apply.
WARNING: this will result in minutes of downtime.
Looks like you’ve already figured it out, but for others that come along:
Newer Dokku Droplets do use the Debian packages, but older ones were installed from source. For convenience on those older Droplets, a local checkout of the Dokku git repository can be found in /root/dokku
To upgrade Dokku, you can run:
cd /root/dokku
git pull --tags origin master
sudo make install