Rewrite WordPress' gallery shortcode output to use markup that's FlexSlider friendly.

flex_gallery_shortcode

<?php

/*
Add this code to functions.php. Then add Woothemes' FlexSlider to your templates 
as you otherwise would.

Rewrite 29 September 2014 to use WordPress filters instead of overwriting the
shortcode handler.

*/

function build_gallery_content( $attrs ){

    static $instance = 0;
    $instance++;

    /* 
    Limiting what the user can do by 
    locking down most short code options.
    */
    extract(shortcode_atts(array(
            'id'         => $post->ID,
            'include'    => '',
            'exclude'    => ''
    ), $attrs));

    $id = intval($id);

    if ( !empty($include) ) {
         $params = array(
                    'include' => $include,
                    'post_status' => 'inherit',
                    'post_type' => 'attachment',
                    'post_mime_type' => 'image',
                    'order' => 'ASC', 
                    'orderby' => 'menu_order ID');
            $_attachments = get_posts( $params );
            $attachments = array();
            foreach ( $_attachments as $key => $val ) {
                    $attachments[$val->ID] = $_attachments[$key];
            }
    } elseif ( !empty($exclude) ) {
            $params = array(
                    'post_parent' => $id,
                    'exclude' => $exclude,
                    'post_status' => 'inherit',
                    'post_type' => 'attachment',
                    'post_mime_type' => 'image',
                    'order' => 'ASC', 
                    'orderby' => 'menu_order ID');
            $attachments = get_children( $params );
    } else {
            $params = array(
                    'post_parent' => $id, 
                    'post_status' => 'inherit', 
                    'post_type' => 'attachment',
                    'post_mime_type' => 'image', 
                    'order' => 'ASC',
                    'orderby' => 'menu_order ID'); 
            $attachments = get_children( $params );
    }

    if ( empty($attachments) )
            return '';

    $selector = "gallery-{$instance}";

    $gallery_div = sprintf("<div class='flexslider'><ul id='%s' class='slides gallery galleryid-%d gallery-columns-1 gallery-size-full'>", $selector, $id);
    $output = $gallery_div;


    foreach ( $attachments as $id => $attachment ) {
        /* 
        Use wp_get_attachment_link to return a photo + link 
        to attachment page or image
        http://codex.wordpress.org/Function_Reference/wp_get_attachment_link 
        */
        $img = wp_get_attachment_image( $id, 'full', false);

        $caption = '';

        /*
        Set the caption string if there is one.
        */

        if( $captiontag && trim($attachment->post_excerpt) ){
            $caption = sprintf("\n\t<figcaption class='wp-caption-text gallery-caption'>\n\t<div>\n%s\n\t</div>\n\t</figcaption>", wptexturize($attachment->post_excerpt));
        }

        /*
        Set the output for each slide.
        */  
        $output .= sprintf("<li class='gallery-item'><figure class='gallery-icon'>%s\n\t%s</figure></li>", $img, $caption);
    }
    $output .= '</ul>\n</div>';
    return $output;
}

function custom_gallery_shortcode( $output = '', $attrs){
    $return = $output;

    # Gallery function that returns new markup.
    $gallery = build_gallery_content( $attrs );


    if( !empty( $gallery ) ) {
        $return = $gallery;
    }

    return $return;
}

add_filter( 'post_gallery', 'custom_gallery_shortcode', 10, 2);