Warn when managing rewrites with --skip-plugins or --skip-themes #3827

WordPress' rewrites API requires the rewrite rules to be registered in order to be saved to the database.

If you run wp rewrite flush with --skip-plugins or --skip-themes, you can inadvertently miss saving rewrites registered in plugins or themes.

To help the user realize their mistake, we should provide a warning when they use wp rewrite * with --skip-plugins or --skip-themes to alert them to the fact that some rewrite rules may be missing.