I'm making a custom theme. It's a highly specialized theme to make WordPress into like an application rather than a CMS system or blog. For instance, a Dental Office Scheduling System (with CMS and widget capabilities), as an example.
Because my theme needs pretty URLs to work properly, something I really need is for the .htaccess file to be that default that gets created only when someone sets Permalinks to Custom (and then types in something like %postname%). How do I trigger that in WordPress, programmatically, so that it creates this? I mean, I could probably overwrite the file myself during theme activation, but the better thing would be to use the WordPress API for it.