From Tims post mortem of the outage overnight:
"WikibaseDataModel returns null from the file level of its extension setup file, causing mergeMessageFileList.php to abort even when the file was present."
Not sure if any other of your extensions are potentially vulnerable due to similar loader code setups
See also 50347
Version: master
Severity: critical
See Also:
https://bugzilla.wikimedia.org/show_bug.cgi?id=50347