This post is a copy from a thread on stackoverflow

It was found that the --tree-filter option used in other answers can be very slow, especially on larger repositories with lots of commits.

Here is the method that one can use to completely remove a directory from the git history using the --index-filter option, which runs much quicker:

• Make a fresh clone of YOUR_REPO

   git clone YOUR_REPO cd YOUR_REPO 
  

• Create tracking branches of all branches

   for remote in `git branch -r | grep -v /HEAD`; do git checkout --track $remote ; done 
  

• Remove DIRECTORY_NAME from all commits, then remove the refs to the old commits (repeat these two commands for as many directories that you want to remove)

   git filter-branch --index-filter 'git rm -rf --quiet --cached --ignore-unmatch DIRECTORY_NAME/' --prune-empty --tag-name-filter cat -- --all git for-each-ref --format="%(refname)" refs/original/ | xargs -n 1 git update-ref -d 
  

• Ensure all old refs are fully removed

   rm -Rf .git/logs .git/refs/original 
  

• Perform a garbage collection to remove commits with no refs

   git gc --prune=all --aggressive 
  

• Force push all branches to overwrite their history (use with caution!)

   git push origin --all --force git push origin --tags --force
  

You can check the size of the repository before and after the gc with:

 git count-objects -vH