Setting permalinks programatically breaks custom post type URL's
|Reported by:||gilbitron||Owned by:|
Using a function to programatically set permalinks (see attached) breaks custom post type URL's. A 404 page is displayed instead.
Visiting the Permalinks settings page fixes the issue (you don't even need to save the permalinks settings).
It turns out that you need to call $wp_rewrite->flush_rules() on the following page load for it to work, even though this is called at the end of the modify_permalinks() function.
Possibly related to #16736