I'm running PhpStorm on a linux box directly, with the target code running in a Vagrant box (running Debian).
When debugging web calls through nginx+fpm, it works properly. When running CLI files, I get the prompt telling me that /vagrant/myfile.php cannot be found locally, to set PHP_IDE_CONFIG blah blah.
It will hit every breakpoints I set, I can inspect variables, it just won't map any files.
This used to work before upgrading to Kubuntu 18.04, which may or may not be related. I tried upgrading from 2017.2 to 2018.1.4, which did not help.
I can debug fine with the same Vagrant box on my Windows 10 host.