Root .gitignore files should generally be checked in.

Removed some non core joomla extensions 
Removed some old joomla 2.5 templates
Removed some index.html no longer present
Removed weblinks component, modules and plugins no longer distributed in the core

update for Joomla 3.3.6

This fixes an issue where index.php within a theme directory would be ignored, when the intention was to just ignore the index.php file in the root.