Updating .htaccess
Updating the .htaccess file that is default in Drupal.  There should not be any host specific settings in this file.  This is so that when we check out the repository it won't give errors about an untracked file with our different .htaccess file in it.
I also had to update the .gitignore to allow the .htaccess file to be added to the repository updating the default one.