Since T329857 was completed, using the staging directory is the only reasonable choice when running scap wikiversions-inuse and scap wikiversions-compile. Currently these tools require the --staging flag to use the staging directory.
To make these tools more friendly in train-dev (where there is not a symlink from /srv/mediawiki to /srv/mediawiki-staging like there is on the real deploy servers), make scap wikiversions-inuse and scap wikiversions-compile default to --staging mode.