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 …