Move JApplication**::getInstance methods to JApplicationBase

This will probably best work with #1769 if it is merged, FYI.

This pull deprecates the getInstance methods of JApplicationCli and JApplicationWeb in favor of having the getInstance method in JApplicationBase.  Generally, only one application can be running properly within a workspace, so this is IMO a logical move to support that theory.  If accepted, this method could theoretically replace JFactory::getApplication (another idea discussed in #1729).