PHPStorm yellow "Method not found in" notices

I don't have the solution but can suggest clicking on the small "man in the hat" icon at the bottom right. There you can configure code inspection.

I do have plugin installed "CodeIgniter" by Martynas Sateika. (Press CTRL+ALT+S > Plugins).

Don't have resolution problems, and didn't have to configure them.

Also in settings you could go to "Languages & Frameowrks > PHP > CodeIgniter" and tick checkbox "Enable CodeIgniter Integration".