Here is a list of all files with brief descriptions:

/home/jason/NetBeansProjects/phpdev/includes/index.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS.inc.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_controller.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_core.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_db.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_debug.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_errorHandler.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_exception.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_legacyConnector.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_login.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_navigation.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_notif.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_pdoConnector.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_query.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_security.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_tagger.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_template.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_user.class.php
/home/jason/NetBeansProjects/phpdev/includes/PHPDS_utils.inc.php
/home/jason/NetBeansProjects/phpdev/plugins/BotBlock/includes/botBlock.class.php
/home/jason/NetBeansProjects/phpdev/plugins/BotBlock/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/ControlPanel/includes/controlPanel.class.php
/home/jason/NetBeansProjects/phpdev/plugins/ControlPanel/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/CRUD/includes/crud.class.php
/home/jason/NetBeansProjects/phpdev/plugins/CRUD/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/FileMan/includes/fileManager.class.php
/home/jason/NetBeansProjects/phpdev/plugins/FileMan/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/Pagination/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/Pagination/includes/pagination.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/groupTree.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/iana.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/menuArray.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/menuStructure.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/pluginManager.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/timeZone.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPDevShell/includes/userPending.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPMailer/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPMailer/includes/mailer.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPThumbs/includes/imaging.class.php
/home/jason/NetBeansProjects/phpdev/plugins/PHPThumbs/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/RedBeanORM/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/RedBeanORM/includes/orm.class.php
/home/jason/NetBeansProjects/phpdev/plugins/Smarty/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/Smarty/includes/views.class.php
/home/jason/NetBeansProjects/phpdev/plugins/StandardLogin/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/StandardLogin/includes/StandardLogin.class.php
/home/jason/NetBeansProjects/phpdev/plugins/TinyMCE/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/TinyMCE/includes/wysiwygEditor.class.php
/home/jason/NetBeansProjects/phpdev/plugins/userActions/includes/index.php
/home/jason/NetBeansProjects/phpdev/plugins/userActions/includes/userActions.class.php