Typo3 now has an official way of overriding Configuration (AdditionalConfiguration.php).
/t3lib has moved into the /typo3 Directory.
Removed v4 specific ignores because it is deprecated and should no longer be used.
There were ignores missing for the symlinked setup.

To make it easier to handle typo3 under git.
There is a related entry at stackoverflow:
http://stackoverflow.com/questions/11905360/how-best-to-manage-typo3-installations-using-git