Remove subfolder from all git history

# 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 --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