Steps to Combine Wordpress and Codeigniter when CI is in a subdirectory of Wordpress

Instructions

Instructions

1. Add MY_url_helper.php to CI_directory/application/helpers

2. If the CI app is already built, convert any references to *site_url* in your CI application (aside from the system directory) to the new namespaced function, ci_site_url.
This step prevents Wordpress' site_url function from overwriting CIs.  Because both functions are global and CI checks to make sure that site_url has not been set.  Once we load the WP bootstrap file, it will have been defined, so CI's function wll never load. 

3. Add Wordpress' bootstrap file into CI_directory/index.php right above CI's bootstrap file.

4. Update wp-includes/load.php *(this is necessary if you are using CI's sessions - Wordpress mangles CI's cookies using with magic quotes. (There may be an upgrade-proof way to do this.)

load.php

<?php
/** wp-includes/load.php */
/** Aproximately line 25 */
	// Variables that shouldn't be unset
	// Add whatever CI's cookie name or, '_SESSION'
	$no_unset = array( 'GLOBALS', '_GET', '_POST', '_COOKIE', '_REQUEST', '_SERVER', '_ENV', '_FILES', 'table_prefix','ci_session' );


/** Approximately line 524 */

/** Add this function */
/**
 * Applies Magic Quotes to the $_COOKIE global but ignores Codeigniter's Cookie
 * @param  string $value Value passed by array_walk function
 * @param  string $key   Key passed by array_walk function
 */
function ci_ignore_magic_quotes($value,$key)
{
	if($key != "ci_session")
	{
		stripslashes_deep($value);
	}
}

/* Update this function */
/**
 * Add magic quotes to $_GET, $_POST, $_COOKIE, and $_SERVER.
 *
 * Also forces $_REQUEST to be $_GET + $_POST. If $_SERVER, $_COOKIE,
 * or $_ENV are needed, use those superglobals directly.
 *
 * @access private
 * @since 3.0.0
 */
function wp_magic_quotes() {
	// If already slashed, strip.
	if ( get_magic_quotes_gpc() ) {
		$_GET    = stripslashes_deep( $_GET    );
		$_POST   = stripslashes_deep( $_POST   );
		$_COOKIE = stripslashes_deep( $_COOKIE );
	}


	// Escape with wpdb.
	$_GET    = add_magic_quotes( $_GET    );
	$_POST   = add_magic_quotes( $_POST   );
	array_walk($_COOKIE, 'ci_ignore_magic_quotes');
	//$_COOKIE = add_magic_quotes( $_COOKIE );
	$_SERVER = add_magic_quotes( $_SERVER );



	// Force REQUEST to be GET + POST.
	$_REQUEST = array_merge( $_GET, $_POST );
}

?>

MY_url_helper.php

<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
/**
 * MY_url_helper.php
 *
 * An open source application development framework for PHP 5.1.6 or newer
 *
 * @package		CodeIgniter
 * @author		Phil Birnie
 * @copyright	Copyright (c) 2013
 * @since		Version 1.0
 * @filesource
 */


// ------------------------------------------------------------------------
// We need to overwrite some of CIs methods that use site_url and replace them with our
// new namespaced function ci_site_url
// ------------------------------------------------------------------------
/**
 * Site URL
 *
 * Create a local URL based on your basepath. Segments can be passed via the
 * first parameter either as a string or an array.
 *
 * @access	public
 * @param	string
 * @return	string
 */
if ( ! function_exists('ci_site_url'))
{
	function ci_site_url($uri = '')
	{
		$CI =& get_instance();
		return $CI->config->site_url($uri);
	}
}


// ------------------------------------------------------------------------

/**
 * Anchor Link
 *
 * Creates an anchor based on the local URL.
 *
 * @access	public
 * @param	string	the URL
 * @param	string	the link title
 * @param	mixed	any attributes
 * @return	string
 */
if ( ! function_exists('anchor'))
{
	function anchor($uri = '', $title = '', $attributes = '')
	{
		$title = (string) $title;

		if ( ! is_array($uri))
		{
			$site_url = ( ! preg_match('!^\w+://! i', $uri)) ? site_url($uri) : $uri;
		}
		else
		{
			$site_url = ci_site_url($uri);
		}

		if ($title == '')
		{
			$title = $site_url;
		}

		if ($attributes != '')
		{
			$attributes = _parse_attributes($attributes);
		}

		return '<a href="'.$site_url.'"'.$attributes.'>'.$title.'</a>';
	}
}

// ------------------------------------------------------------------------

/**
 * Anchor Link - Pop-up version
 *
 * Creates an anchor based on the local URL. The link
 * opens a new window based on the attributes specified.
 *
 * @access	public
 * @param	string	the URL
 * @param	string	the link title
 * @param	mixed	any attributes
 * @return	string
 */
if ( ! function_exists('anchor_popup'))
{
	function anchor_popup($uri = '', $title = '', $attributes = FALSE)
	{
		$title = (string) $title;

		$site_url = ( ! preg_match('!^\w+://! i', $uri)) ? ci_site_url($uri) : $uri;

		if ($title == '')
		{
			$title = $site_url;
		}

		if ($attributes === FALSE)
		{
			return "<a href='javascript:void(0);' onclick=\"window.open('".$site_url."', '_blank');\">".$title."</a>";
		}

		if ( ! is_array($attributes))
		{
			$attributes = array();
		}

		foreach (array('width' => '800', 'height' => '600', 'scrollbars' => 'yes', 'status' => 'yes', 'resizable' => 'yes', 'screenx' => '0', 'screeny' => '0', ) as $key => $val)
		{
			$atts[$key] = ( ! isset($attributes[$key])) ? $val : $attributes[$key];
			unset($attributes[$key]);
		}

		if ($attributes != '')
		{
			$attributes = _parse_attributes($attributes);
		}

		return "<a href='javascript:void(0);' onclick=\"window.open('".$site_url."', '_blank', '"._parse_attributes($atts, TRUE)."');\"$attributes>".$title."</a>";
	}
}




// ------------------------------------------------------------------------

/**
 * Header Redirect
 *
 * Header redirect in two flavors
 * For very fine grained control over headers, you could use the Output
 * Library's set_header() function.
 *
 * @access	public
 * @param	string	the URL
 * @param	string	the method: location or redirect
 * @return	string
 */
if ( ! function_exists('redirect'))
{
	function redirect($uri = '', $method = 'location', $http_response_code = 302)
	{
		if ( ! preg_match('#^https?://#i', $uri))
		{
			$uri = ci_site_url($uri);
		}

		switch($method)
		{
			case 'refresh'	: header("Refresh:0;url=".$uri);
				break;
			default			: header("Location: ".$uri, TRUE, $http_response_code);
				break;
		}
		exit;
	}
}


/* End of file MY_url_helper.php */
/* Location: ./application/helpers/MY_url_helper.php */