Git-ignore directives for OS-specific files and IDE-specific files should go in the environment's global .gitignore file.  See http://stackoverflow.com/questions/1753070/git-ignore-files-only-locally
Ignore files/ directory and settings.php.
Version control default.settings.php to make it easier to notice Drupal core updates that affect settings.php.
Move the Nesi Bootstrap subtheme into it's own directory.
Remove bootstrap contrib theme and third party libraries from repository since they should be managed in make file.
Drupal core update to default.settings.php.
Move custom/ directory wrapping custom modules.