After lots of debugging of an apparent wiki misconfiguration issue, I found that early on when Vagrant loads /var/www/w/dblist.php, and that file calls glob( '/vagrant/settings.d/wikis/dbConf/*dbConf.php' ), /vagrant/settings.d/wikis/dbConf/10-wiki-dbConf.php is not picked up (and so $wgLocalDatabases will be left empty and the site will fail to load). The file looks normal:
vagrant@mediawikivagrant:~$ ls -l /vagrant/settings.d/wikis/dbConf/*dbConf.php -rw-r--r-- 1 vagrant_share vagrant_share 226 Sep 12 23:12 /vagrant/settings.d/wikis/dbConf/10-wiki-dbConf.php
although I don't quite get why it's owned by vagrant_share, but both the vagrant and www-data users can see it, and accessing it from PHP also works in most contexts (e.g. shell.php, plain CLI, built-in server with php -s). The web-based PHP processes don't see it though:
var_dump(['u' => get_current_user(), 'glob' => glob( '/vagrant/settings.d/wikis/dbConf/*dbConf.php' ), 'c' => file_get_contents('/vagrant/settings.d/wikis/dbConf/10-wiki-dbConf.php') ]);
Warning: file_get_contents(/vagrant/settings.d/wikis/dbConf/10-wiki-dbConf.php): failed to open stream: No such file or directory in /var/www/w/dblist.php on line 9
array (size=3)
'u' => string 'vagrant' (length=7)
'glob' =>
array (size=0)
empty
'c' => boolean false