What PeterT said
Images would be where you would place an a: Alternate Trashcan icon.
Calibre will look at resources/images FIRST
if the file it wants for the UI, exists there, it uses that one.: else, it uses the Programs/resources/images one.
(user)Plugins always use the configuration folder

the calibre2 folder is 'Vanilla Calibre'
the configuration folders are the added 'Toppings'