CPT and rewrite rules

Finally, found a solution mix:

The CPT has to have:

 'has_archive'         => 'library', // Fixes the archive URL.
 'rewrite'             => array(
    'slug'       => 'library/%library-category%',
    'with_front' => false,
 )

Taxonomy should be as following:

'rewrite'        => array(
    'slug'       => 'library',
    'with_front' => false,
),

And than you need to rewrite the links:

/**
 * Custom rewrite rules for URL
 *
 * @param string  $post_link Post link url.
 * @param integer $id Post ID.
 * @return string
 */
function getmanta_technologies_post_link( $post_link, $id = 0 ) {
    $post = get_post( $id );
    if ( is_object( $post ) ) {     
        $terms_lc = wp_get_object_terms( $post->ID, 'library-category' );
        if ( $terms_lc ) {
            return str_replace( '%library-category%', $terms_lc[0]->slug, $post_link );
        }
    }
    return $post_link;
}
add_filter( 'post_type_link', 'getmanta_technologies_post_link', 1, 3 );