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The procedure is very similar to delete .DS_Store File . You can delete .ipynb_checkpoints folder this way: find . -name .ipynb_checkpoints -print0 | xargs -0 git rm -rf --ignore-unmatch git add . git commit -m "Remove .ipynb_checkpoints from everywhere" git push Then you can ignore all future .ipynb_checkpoints this way: touch .gitignore echo \.ipynb_checkpoints >> .gitignore git add . git commit -m "Creating .gitignore and ignore .ipynb_checkpoints" git push...