Fixes missing ul from #2904

The overridden menu_tree function was returning the tree before adaptivetheme could wrap it with a ul.  This was fine for nice_menus, but incorrect everywhere else.  There weren't any useful vars at this point, so I had to add a flag os_basetheme_menu_tree could check to see if nice_menus were in use.  I added this in preprocess_menu_tree, but it was being stripped before I could get to it by core's template_preprocess_menu_tree.  I had to remove it via hook_theme_registry_alter and then duplicate its functionality in my funciton.  This was a little more roundabout than intended, but I can't think of anything cleaner at this point.
Removed dev code.  #2904
Merge pull request #3046 from openscholar/2904-ul_fix

2904 ul fix