How do I ignore certain files while debugging in PHPStorm?

There are settings in Languages & Frameworks > PHP > Debug that allow you to remove the break-at-first-line behavior and ignore unregistered connections.

One possible solution is to add the following parameters to the bat file that runs phpcs:

-d xdebug.remote_host="8.8.1.1" \
-d xdebug.remote_enable=0 \
-d xdebug.remote_autostart=0

This sets custom PHP ini settings on the command line interface.

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Alternately, go to Settings | PHP | Debug in PHPStorm and add a directory to the debug ignore list.

You can ignore a file in PhpStorm in:

Preferences > PHP > Debug > Step Filters

Add it with the + sign in the skipped files section and navigate to the folder containing the file.