Running `vagrant git-update` with the `wikibase` role enabled gives me this:
```
[d6082a1b37919ea1f563e7a7] [no req] Error from line 35 of /vagrant/mediawiki/extensions/Wikibase/lib/WikibaseLib.entitytypes.php: Class 'Wikibase\DataModel\Entity\ItemId' not found
Backtrace:
#0 /vagrant/mediawiki/extensions/Wikibase/repo/includes/WikibaseRepo.php(566): require()
#1 /vagrant/mediawiki/extensions/Wikibase/repo/includes/WikibaseRepo.php(312): Wikibase\Repo\WikibaseRepo::getDefaultEntityTypes()
#2 /vagrant/mediawiki/extensions/Wikibase/repo/includes/WikibaseRepo.php(370): Wikibase\Repo\WikibaseRepo::newInstance()
#3 /vagrant/mediawiki/extensions/Wikibase/repo/RepoHooks.php(100): Wikibase\Repo\WikibaseRepo::getDefaultInstance()
#4 /vagrant/mediawiki/includes/Hooks.php(174): Wikibase\RepoHooks::onSetupAfterCache()
#5 /vagrant/mediawiki/includes/Hooks.php(202): Hooks::callHook(string, array, array, NULL)
#6 /vagrant/mediawiki/includes/Setup.php(791): Hooks::run(string)
#7 /vagrant/mediawiki/maintenance/doMaintenance.php(81): require_once(string)
#8 /vagrant/mediawiki/maintenance/update.php(245): require_once(string)
#9 /var/www/w/MWScript.php(98): require_once(string)
#10 {main}
```
The missing class gets installed by Composer, and is included in the autoloader classmap generated by Composer, so presumably that classmap does not get loaded. See the `load_composer_autoloader` property in `extension.json` for how that's normally done.