The refresh lived inside "System update", which `step` skips when its name is
already in the progress file. So a resumed run — the common case, since that is
what the progress file is for — installed core utils, added the fastfetch PPA and
set up the Docker repo against whatever the index happened to say hours or days
earlier. On a box left overnight that is a stale index and a "package not found"
somewhere unrelated.
It now runs in pre-flight, unconditionally, before any step exists to skip it.
`apt-get upgrade` stays where it was and stays confirmable: refreshing the index
changes nothing on the machine, upgrading is the one thing that does.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>