[Plugin: Category Template Hierarchy] Works with custom taxonomies?

No it does not. However, given a recent change to another plugin of mine, it makes sense that I should do the same to this one, and give developers the ability to choose the taxonomy.

… or better yet, simply allow it to work with any taxonomy.

I will make this the next version of this plugin. I will respond to this thread when I am able to make those changes and release them.

Thanks for the suggestion.