There are two base phan configurations for MediaWiki projects:
config.php
for MediaWiki code, like extensions and skinsconfig-library.php
for PHP libraries and other code external to MediaWiki
Choose the file more suitable for your project, then include it in the phan configuration and extend/modify it as you see fit.
See https://www.mediawiki.org/wiki/Continuous_integration/Phan for more details.