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I have created a custom post type where in one of the metaboxes I have checkboxes where author can select what he would like to add on the post.

Now, if the author wants to add something that is not already there they should be able to click an "add new" button where they would be presented with options to add their own checkbox. What would be the standard WordPress method of doing that?

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Your question is very abstract. As far I understood you want some thing like categories.enter image description here

So for that adding metaboxes is not necessary. I think categories are enough. If categories are not full filling your need then make another custom taxonomy with 'hierarchical' => true,. I think it will serve your need. Also giving permissions to author to create dynamic meta box is not a good idea. So first try with category otherwise custom taxonomy. "Author can create dynamic meta boxes" is your last option.

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Try use ACF (advanced custom fields) plugin... It have similar option to what you are asking for

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