Program: CWE-79
Project: CVE-2014-4853
Buggy source:
<?php
/*
init.php - bootloader to initialize variables
 * If the config.php file is not found then an error
 * will be displayed asking the visitor to set up the
 * config.php file.
 *
 * Will also search for config.php in the OpenDocMan parent
 * directory to allow the OpendocMan directory to remain
 * untouched.

Copyright (C) 2011 Stephen Lawrence Jr.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

/*
 * Connect to Database
 */
$GLOBALS['connection'] = mysql_connect(DB_HOST, DB_USER, DB_PASS) or die ("Unable to connect: " . mysql_error());
$db = mysql_select_db(DB_NAME, $GLOBALS['connection']);

$dsn = "mysql:host=" . DB_HOST . ";dbname=" . DB_NAME . ";charset=utf8";
try {
    $pdo = new PDO($dsn, DB_USER, DB_PASS);
} catch (PDOException $e) {
    print "Error!: " . $e->getMessage() . "<br/>";
    die();
}

$GLOBALS['pdo'] = $pdo;

ob_start();
include('includes/FirePHPCore/fb.php');

/*
/*
 * Load the Settings class
 */
require_once ( 'Settings_class.php');
$settings = new Settings();
$settings->load();

/*
 * Common functions
 */
require_once( 'functions.php' );

/*
 * Load the allowed file types list
 */
require_once ( 'FileTypes_class.php' );
$filetypes = new FileTypes_class();
$filetypes->load();

// Set the revision directory. (relative to $dataDir)
$CONFIG['revisionDir'] = $GLOBALS['CONFIG']['dataDir'] . 'revisionDir/';

// Set the revision directory. (relative to $dataDir)
$CONFIG['archiveDir'] = $GLOBALS['CONFIG']['dataDir'] . 'archiveDir/';

$_GET = sanitizeme($_GET);
$_REQUEST = sanitizeme($_REQUEST);
$_POST = sanitizeme($_POST);
$_SERVER = sanitizeme($_SERVER);


Fixed version (ground truth):
<?php
/*
init.php - bootloader to initialize variables
 * If the config.php file is not found then an error
 * will be displayed asking the visitor to set up the
 * config.php file.
 *
 * Will also search for config.php in the OpenDocMan parent
 * directory to allow the OpendocMan directory to remain
 * untouched.

Copyright (C) 2011 Stephen Lawrence Jr.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

/*
 * Connect to Database
 */
$GLOBALS['connection'] = mysql_connect(DB_HOST, DB_USER, DB_PASS) or die ("Unable to connect: " . mysql_error());
$db = mysql_select_db(DB_NAME, $GLOBALS['connection']);

$dsn = "mysql:host=" . DB_HOST . ";dbname=" . DB_NAME . ";charset=utf8";
try {
    $pdo = new PDO($dsn, DB_USER, DB_PASS);
} catch (PDOException $e) {
    print "Error!: " . $e->getMessage() . "<br/>";
    die();
}

$GLOBALS['pdo'] = $pdo;

ob_start();
include('includes/FirePHPCore/fb.php');

/*
/*
 * Load the Settings class
 */
require_once ( 'Settings_class.php');
$settings = new Settings();
$settings->load();

/*
 * Common functions
 */
require_once( 'functions.php' );

/*
 * Load the allowed file types list
 */
require_once ( 'FileTypes_class.php' );
$filetypes = new FileTypes_class();
$filetypes->load();

// Set the revision directory. (relative to $dataDir)
$CONFIG['revisionDir'] = $GLOBALS['CONFIG']['dataDir'] . 'revisionDir/';

// Set the revision directory. (relative to $dataDir)
$CONFIG['archiveDir'] = $GLOBALS['CONFIG']['dataDir'] . 'archiveDir/';

$_GET = sanitizeme($_GET);
$_REQUEST = sanitizeme($_REQUEST);
$_POST = sanitizeme($_POST);
$_SERVER = sanitizeme($_SERVER);
$_FILES = sanitizeme($_FILES);