It is used by wp-cli, the command line interface for WordPress.
wp-cli.yml is where you set configuration values, related to your website, for wp-cli.php to use.
For example, to update "pretty links" from the command line (
wp rewrite flush), the
wp-cli.yml (or a
config.yml) file is necessary for the command to work properly.
From the docs:
wp rewrite flush flushes rewrite rules.
Resets WordPress’ rewrite rules based on registered post types, etc.
To regenerate a
.htaccess file with WP-CLI, you’ll need to add the
mod_rewrite module to your
Flushing and Re-saving permalinks is often needed when changing themes, or if you change the installation folder for your WordPress files.