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phan failing for Wikibase on wmf. branches
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Description

Example: https://gerrit.wikimedia.org/r/#/c/mediawiki/extensions/Wikibase/+/440295/

This is due to the extension directories existing for core on the wmf branches

Checks for these directories in the phan config then do the wrong thing
https://github.com/wikimedia/mediawiki-extensions-Wikibase/blob/master/tests/phan/config.php#L62-L67
https://github.com/wikimedia/mediawiki-extensions-Wikibase/blob/master/tests/phan/config.php#L97-L102

These checks need to be modified, perhaps just to make sure that the directory is not totally empty.