Script from http://dound.com/2009/04/git-forever-remove-files-or-folders-from-history/

git-delete-history.sh

#!/bin/bash
set -o errexit
 
# Author: David Underhill
# Script to permanently delete files/folders from your git repository.  To use 
# it, cd to your repository's root and then run the script with a list of paths
# you want to delete, e.g., git-delete-history path1 path2
 
if [ $# -eq 0 ]; then
    exit 0
fi
 
# make sure we're at the root of git repo
if [ ! -d .git ]; then
    echo "Error: must run this script from the root of a git repository"
    exit 1
fi
 
# remove all paths passed as arguments from the history of the repo
files=$@
git filter-branch --prune-empty --index-filter "git rm -rf --cached --ignore-unmatch $files" HEAD
 
# remove the temporary history git-filter-branch otherwise leaves behind for a long time
rm -rf .git/refs/original/ && git reflog expire --all &&  git gc --aggressive --prune
git repack -A -d