Add tests which cover --apply #1419
Description
We are missing tests here which cover upgrade --apply and hence the reboot flow we initiate which would have caught #1416
To fix this in the tmt tests we probably need to add tmt-reboot-prepare; actually I filed teemtee/tmt#3886
That said we can and should cover this with a testing flow that runs outside of tmt; actually I'd like to have some of our tests create machines which don't run ssh at all and report their status instead of being puppeted over ssh. Something like an "e2e-upgrade" test that runs a complete scenario instead of being synthetic too, i.e. run a representative workload.
Of course more ideally tmt would support something like that, but it'd be a pretty fundamental change for it AFAIK.