Add apply flag to praefect remove repo e2e
What does this MR do and why?
gitaly!4054 (merged) changed the behaviour of remove-repo to be a 'dry-run' meaning users would need to add an 'apply' flag to the commands. This change adds that flag into the e2e tests
The flag needs to be also applied in omnibus so requires omnibus-gitlab!5785 (merged)
Edited by John McDonnell