I tried to test a maintenence script on Beta Cluster (ssh-ed into deployment-bastion.eqiad.wmflabs):
mwscript extensions/Flow/maintenance/FlowFixEditCount.php --wiki=enwiki
It prompts for my password, which of course I don't know.
It turns out (thanks @Krenair) that the workaround is:
sudo mwscript extensions/Flow/maintenance/FlowFixEditCount.php --wiki=enwiki
but this seems unnecessary (there is already logic in the script about doing sudo, so it should work).
(obviously the workaround is for projectadmins only, and shouldn't really be encouraged... although this is beta so...)
The current mwscript still tries to sudo apache and normal users no longer have that right in beta. The script should be changed in operations/puppet.git to sudo www-data instead but that will require Ops intervention and probably applying the apache -> www-data file ownership conversions of T78076 on tin and terbium.
The ability to run commands as the "apache" user has been removed from the prod admins module today.