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Rename .phpstorm.meta.php* files. There are old file version. And new folder version. Also these files are in project root directory and in subdirectory called sub — to check that one file extends another.
Run PhpStorm action: Invalidate Caches / Restart, then click Invalidate and Restart.
My observations about .phpstorm.meta.php
Autocompletion is broken when root format is not the same with subfolder format (for example, file /.phpstorm.meta.php and folder /sub/.phpstorm.meta.php/ with locators.php and vice versa).
When format is the same then configurations extend each other. So definitions from root /.phpstorm.meta.php will sum up with /sub/.phpstorm.meta.php.