run: use subprocess.run(check=True) by default

We ignore failures all too often, leading to spririses much further down
the road. Let's croak on unexpected failures by default and explicitely
ignore them wherever unexpected.
4 jobs for !883 with lr/run-check in 1 minute and 16 seconds (queued for 1 second)
latest detached
Status Name Job ID Coverage
  Test
manual TestResults #16244405
manual
passed UnitTests #16244404

00:01:16

 
  External
failed https://desktopqe-jenkins.rhev-ci-vms.eng.rdu2.redhat.com/job/beaker-NetworkManager-gitlab-trigger-test-upstream/2060/

failed https://desktopqe-jenkins.rhev-ci-vms.eng.rdu2.redhat.com/job/beaker-NetworkManager-gitlab-trigger-test-upstream/2060/

02:14:08