You can enable Extra Fields for Folders for the icon url, than custom code the gallery output.
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Also this could be done with folder Featured Images (not supported yet) and custom gallery output to exclude this image from the attachments.
see: http://wordpress.org/support/topic/featured-image-113
You can use also the eazyest_gallery_folder_icon filter.
The plugin uses that filter for the folder icon:
$icon = apply_filters( ‘eazyest_gallery_folder_icon’, eazyest_gallery()->plugin_url . ‘frontend/images/folder-icon.png’ );
WordPress page about how to add filters:
http://codex.wordpress.org/Function_Reference/add_filter
The code for your functions.php:
// Custom folder icon thumbnail
function custom_folder_icon() {
return 'custom/path/to/image.jpg';
}
add_filter('eazyest_gallery_folder_icon','custom_folder_icon');