I just updated Drupal to 7.39 using Drush, in particular the command
drush up and all related steps as explained here: https://www.drupal.org/node/2550801.
During the update I have noticed this extremely worrying line, saying that Drush is messing with my .git directory:
So I got back the .git folder from the backup created by the Drush updater, committed and pushed.
The problem is that Drush, without any warning, not only corrupted the .git directory but also messed with my .gitignore file, deleting several lines.
As a result I pushed a very large number of cache and temporary files to my company's git repo and had to later fix it and apologise to my colleagues.
My question is: is there a way to update Drupal programmatically (no admin or manually moving files) without Drush trying to destroy my git repo?