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.
Caused by rEWBA505e4860cc72: Remove optional dependency on Wikibase local vendor directory.