Codeigniter and Wordpress link up

I have been Using these instructions: https://github.com/AdeptMarketing/Wordpress_CI so that we can add the correct navigation etc to the codeigniter area of a website.

The codeigniter application has just been updated and works correctly on a seperate dev url - it is a basic booking system that allows users to register and book available slots in a diary, and for and admin to login and activate users and approve the bookings.  Now that I have followed the above instructions to move the application into the wordpress system there is an issue with user activation where the url is changing to the direct wordpress url and returning a 404 rather than the /ice-diary/index.php/auth this is the activate function within codeigniter:

PHP Code:

    //activate the user
    function activate($id, $code=false)
    {
        if ($code !== false)
        {
            $activation = $this->ion_auth->activate($id, $code);
        }
        else if ($this->ion_auth->is_admin())
        {
            $activation = $this->ion_auth->activate($id);
        }

        if ($activation)
        {
            //redirect them to the auth page
            $this->session->set_flashdata('message', $this->ion_auth->messages());
            redirect("auth", 'refresh');
        }
        else
        {
            //redirect them to the forgot password page
            $this->session->set_flashdata('message', $this->ion_auth->errors());
            redirect("auth/forgot_password", 'refresh');
        }
    } 


How do I get the correct auth url back? New to codeigniter, this is the first project I have worked on so any help would be really appreciated.
Many Thanks

I figured this out, I had to edit the anchors in the template file, thanks for looking :-)

thanks for figured out this, I will use for my site. *SEO SPAM LINK REDACTED*