Some tools for analyzing the files (also deleted files) in the repo and removing them completely from history. Warning: black magic is involved, and the commit hashes will be changed.

git_black_magic.py

#!/usr/bin/env python3
 
"""
Functionality for cleaning up your git repository.
 
This uses commands found on:
https://help.github.com/articles/remove-sensitive-data
 
"""
 
import os
import sys
import subprocess
 
 
def call(cmd):
    subprocess.call(cmd, shell=True)
 
 
def remove(path):
    """ Remove the given path (file or directory) from the history
    of this repository.
    """
    command = ("git filter-branch --force --index-filter " +
    "'git rm -r --cached --ignore-unmatch %s' " +
    "--prune-empty --tag-name-filter cat -- --all")
    call(command%path)
 
def clean():
    """ Clean the backup branch that was created during the remove step.
    """
    call("git update-ref -d refs/original/refs/heads/master")
    call("git reflog expire --expire=now --all")
    call("git gc --prune=now")
 
 
def deleted():
    """ Get a list of all deleted objects know by the repo.
    """
    subprocess.call("git log --diff-filter=D --summary | grep delete", shell=True)
    
 
def all():
    """ Get a list of all files that were ever in the repo.
    """
    subprocess.call("git rev-list --objects --all | sort -k 2 | cut -f 2 -d\ | uniq", shell=True)
 
 
def sizes(maxcount=20):
    """ Get a list of the N biggest files in the repo (and show their size in bytes).
    """
    # Clear
    for fname in ['bigtosmall.txt', 'allfileshas.txt', 'bigobjects.txt']:
        if os.path.isfile(fname):
            os.remove(fname)
    # Git commands
    call("git rev-list --objects --all | sort -k 2 > allfileshas.txt")
    call('git gc && git verify-pack -v .git/objects/pack/pack-*.idx | egrep "^\w+ blob\W+[0-9]+ [0-9]+ [0-9]+$" | sort -k 3 -n -r > bigobjects.txt')
    call("for SHA in `cut -f 1 -d\ < bigobjects.txt`; do\necho $(grep $SHA bigobjects.txt) $(grep $SHA allfileshas.txt) | awk '{print $1,$3,$7}' >> bigtosmall.txt\ndone;")
    # Show results
    with open('bigtosmall.txt', 'r') as f:
        count = 0
        for line in f.readlines():
            count += 1
            print(line.strip().split(' ',1)[1])
            if count >= maxcount:
                return
 
 
if __name__ == '__main__':
    if sys.argv[1] == 'remove':
        remove(sys.argv[2])
    elif sys.argv[1] == 'clean':
        clean()
    elif sys.argv[1] == 'deleted':
        deleted()
    elif sys.argv[1] == 'all':
        all()
    elif sys.argv[1] == 'sizes':
        if len(sys.argv) > 2:
            sizes(int(sys.argv[2]))
        else:
            sizes()
    else:
        print('Invalid command')