Problem: Remove multiple deleted files in Git repo Note that '~$' stands for root directory in your terminal Solutions: This command will ONLY remove the deleted files from the git: ~$ git rm $(git ls-files --deleted) Update all your changes using(Read note above!) ~$ git add -u changed in Git 2.0 and should not be used anymore! Another hint for for adding ONLY modified files: ~$ git add $(git ls-files --modified)