In the FAQ, it's clearly stated that this behavior will not change (http://manual.calibre-ebook.com/faq.html#why-doesn-t-app-let-me-store-books-in-my-own-direct

In the FAQ, it's clearly stated that this behavior will not change (http://manual.calibre-ebook.com/faq.html#why-doesn-t-app-let-me-store-books-in-my-own-directory-structure http://manual.calibre-ebook.com/faq.html#why-doesn-t-app-let...). And this is also the reason why I'm not using Calibre as a library manager (I occasionally use the command line tools). I would regularly donate to a FOSS ebook library manager that does library management (I would rather use other tools to make my morning coffee).