[#33850] You can't set a config array in the Application

http://joomlacode.org/gf/project/joomla/tracker/?action=TrackerItemEdit&tracker_item_id=33850&start=0

Allow the ```$config``` param to continue to work from the JFactory::getApplication() function or the legacy JApplication::getInstance() function.

JApplicationCms has a ```$config``` param in the constructor but not in the ```getInstance()``` function. This PR adds that support in and stops the config from being immediately overwritten when the app is initalised. Note that the config (from ```JFactory::getConfig()``` still takes priority over anything initialised in the app's constructor however.

For testing instructions see the tracker item