When rebuilding the staging area, we had a bunch of files left over that are not in /private/:
$ diff -u /srv/mediawiki/wmf-config /srv/mediawiki-staging/wmf-config Only in /srv/mediawiki/wmf-config: contribution-tracking-setup.php Only in /srv/mediawiki/wmf-config: keys.txt Only in /srv/mediawiki/wmf-config: mwblocker.log Only in /srv/mediawiki/wmf-config: .svn Only in /srv/mediawiki/wmf-config: x.php Only in /srv/mediawiki/wmf-config: xrumer $
We should migrate them all under /private/