For all practical purposes, the first thing you should be worried about is CHANGING YOUR PASSWORDS! It’s not clear from your question whether your git repository is entirely local or whether you have a remote repository elsewhere yet; if it is remote and not secured from others you have a problem. If anyone has cloned that repository before you fix this, they’ll have a copy of your passwords on their local machine, and there’s no way you can force them to update to your “fixed” version with it gone from history. The only safe thing you can do is change your password to something else everywhere you’ve used it.

With that out of the way, here’s how to fix it. GitHub answered exactly that question as an FAQ:

Note for Windows users: use double quotes (“) instead of singles in this command

git filter-branch --index-filter 
'git update-index --remove PATH-TO-YOUR-FILE-WITH-SENSITIVE-DATA' <introduction-revision-sha1>..HEAD
git push --force --verbose --dry-run
git push --force

Update 2019:

This is the current code from the FAQ:

  git filter-branch --force --index-filter 
  "git rm --cached --ignore-unmatch PATH-TO-YOUR-FILE-WITH-SENSITIVE-DATA" 
  --prune-empty --tag-name-filter cat -- --all
  git push --force --verbose --dry-run
  git push --force

Keep in mind that once you’ve pushed this code to a remote repository like GitHub and others have cloned that remote repository, you’re now in a situation where you’re rewriting history. When others try pull down your latest changes after this, they’ll get a message indicating that the changes can’t be applied because it’s not a fast-forward.

To fix this, they’ll have to either delete their existing repository and re-clone it, or follow the instructions under “RECOVERING FROM UPSTREAM REBASE” in the git-rebase manpage.

Tip: Execute git rebase --interactive

In the future, if you accidentally commit some changes with sensitive information but you notice before pushing to a remote repository, there are some easier fixes. If you last commit is the one to add the sensitive information, you can simply remove the sensitive information, then run:

git commit -a --amend

That will amend the previous commit with any new changes you’ve made, including entire file removals done with a git rm. If the changes are further back in history but still not pushed to a remote repository, you can do an interactive rebase:

git rebase -i origin/master

That opens an editor with the commits you’ve made since your last common ancestor with the remote repository. Change “pick” to “edit” on any lines representing a commit with sensitive information, and save and quit. Git will walk through the changes, and leave you at a spot where you can:

$EDITOR file-to-fix
git commit -a --amend
git rebase --continue

For each change with sensitive information. Eventually, you’ll end up back on your branch, and you can safely push the new changes.

Changing your passwords is a good idea, but for the process of removing password’s from your repo’s history, I recommend the BFG Repo-Cleaner, a faster, simpler alternative to git-filter-branch explicitly designed for removing private data from Git repos.

Create a private.txt file listing the passwords, etc, that you want to remove (one entry per line) and then run this command:

$ java -jar bfg.jar  --replace-text private.txt  my-repo.git

All files under a threshold size (1MB by default) in your repo’s history will be scanned, and any matching string (that isn’t in your latest commit) will be replaced with the string “***REMOVED***”. You can then use git gc to clean away the dead data:

$ git gc --prune=now --aggressive

The BFG is typically 10-50x faster than running git-filter-branch and the options are simplified and tailored around these two common use-cases:

• Removing Crazy Big Files
• Removing Passwords, Credentials & other Private data

Full disclosure: I’m the author of the BFG Repo-Cleaner.

git filter-repo is now officially recommended over git filter-branch

This is mentioned in the manpage of git filter-branch in Git 2.5 itself.

With git filter repo, you could either remove certain files with: Remove folder and its contents from git/GitHub’s history

pip install git-filter-repo
git filter-repo --path path/to/remove1 --path path/to/remove2 --invert-paths

This automatically removes empty commits.

Or you can replace certain strings with: How to replace a string in whole Git history?

git filter-repo --replace-text <(echo 'my_password==>xxxxxxxx')

If you pushed to GitHub, force pushing is not enough, delete the repository or contact support

Even if you force push one second afterwards, it is not enough as explained below.

The only valid courses of action are:

• is what leaked a changeable credential like a password?

  • yes: modify your passwords immediately, and consider using more OAuth and API keys!

  • no (naked pics):

    • do you care if all issues in the repository get nuked?

      • no: delete the repository

      • yes:

        • contact support
        • if the leak is very critical to you, to the point that you are willing to get some repository downtime to make it less likely to leak, make it private while you wait for GitHub support to reply to you

Force pushing a second later is not enough because:

• GitHub keeps dangling commits for a long time.

  GitHub staff does have the power to delete such dangling commits if you contact them however.

  I experienced this first hand when I uploaded all GitHub commit emails to a repo they asked me to take it down, so I did, and they did a gc. Pull requests that contain the data have to be deleted however: that repo data remained accessible up to one year after initial takedown due to this.

  Dangling commits can be seen either through:

  • the commit web UI: https://github.com/cirosantilli/test-dangling/commit/53df36c09f092bbb59f2faa34eba15cd89ef8e83 (Wayback machine)
  • the API: https://api.github.com/repos/cirosantilli/test-dangling/commits/53df36c09f092bbb59f2faa34eba15cd89ef8e83 (Wayback machine)

  One convenient way to get the source at that commit then is to use the download zip method, which can accept any reference, e.g.: https://github.com/cirosantilli/myrepo/archive/SHA.zip

• It is possible to fetch the missing SHAs either by:

  • listing API events with type": "PushEvent". E.g. mine: https://api.github.com/users/cirosantilli/events/public (Wayback machine)
  • more conveniently sometimes, by looking at the SHAs of pull requests that attempted to remove the content

• There are scrappers like http://ghtorrent.org/ and https://www.githubarchive.org/ that regularly pool GitHub data and store it elsewhere.

  I could not find if they scrape the actual commit diff, and that is unlikely because there would be too much data, but it is technically possible, and the NSA and friends likely have filters to archive only stuff linked to people or commits of interest.

If you delete the repository instead of just force pushing however, commits do disappear even from the API immediately and give 404, e.g. https://api.github.com/repos/cirosantilli/test-dangling-delete/commits/8c08448b5fbf0f891696819f3b2b2d653f7a3824 This works even if you recreate another repository with the same name.

To test this out, I have created a repo: https://github.com/cirosantilli/test-dangling and did:

git init
git remote add origin [email protected]:cirosantilli/test-dangling.git

touch a
git add .
git commit -m 0
git push

touch b
git add .
git commit -m 1
git push

touch c
git rm b
git add .
git commit --amend --no-edit
git push -f

See also: How to remove a dangling commit from GitHub?

You can use git forget-blob.

The usage is pretty simple git forget-blob file-to-forget. You can get more info here:

• GitHub: nachoparker/git-forget-blob

It will disappear from all the commits in your history, reflog, tags and so on

I run into the same problem every now and then, and everytime I have to come back to this post and others, that’s why I automated the process.

Credits to contributors from Stack Overflow that allowed me to put this together

I recommend this script by David Underhill, worked like a charm for me.

It adds these commands in addition natacado’s filter-branch to clean up the mess it leaves behind:

rm -rf .git/refs/original/
git reflog expire --all
git gc --aggressive --prune

Full script (all credit to David Underhill)

#!/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 --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

The last two commands may work better if changed to the following:

git reflog expire --expire=now --all && 
git gc --aggressive --prune=now

Here is my solution on Windows:

git filter-branch --tree-filter "rm -f 'filedir/filename'" HEAD

git push --force

Make sure that the path is correct.
Otherwise it won’t work.

Use filter-branch:

git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch *file_path_relative_to_git_repo*' --prune-empty --tag-name-filter cat -- --all

git push origin *branch_name* -f

To be clear: The accepted answer is correct. Try it first. However, it may be unnecessarily complex for some use cases, particularly if you encounter obnoxious errors such as ‘fatal: bad revision –prune-empty’, or really don’t care about the history of your repo.

An alternative would be:

1. cd to project’s base branch
2. Remove the sensitive code / file
3. rm -rf .git/ # Remove all git info from
   your code
4. Go to github and delete your repository
5. Follow this guide to push your code to a new repository as you normally would –
   https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/

This will of course remove all commit history branches, and issues from both your github repo, and your local git repo. If this is unacceptable you will have to use an alternate approach.

Call this the nuclear option.

In my Android project, I had admob_keys.xml as separated XML file in app/src/main/res/values/ folder. To remove this sensitive file, I used the below script, and it worked perfectly.

git filter-branch --force --index-filter 
'git rm --cached --ignore-unmatch  app/src/main/res/values/admob_keys.xml' 
--prune-empty --tag-name-filter cat -- --all

I’ve had to do this a few times to-date. Note that this only works on 1 file at a time.

1. Get a list of all commits that modified a file. The one at the bottom will the the first commit:

   git log --pretty=oneline --branches -- pathToFile

2. To remove the file from history use the first commit sha1 and the path to file from the previous command, and fill them into this command:

   git filter-branch --index-filter 'git rm --cached --ignore-unmatch <path-to-file>' -- <sha1-where-the-file-was-first-added>..

Considering that OP is using GitHub, if one commits sensitive data into a Git repo, one can remove it entirely from the history by using one of the previous options (read more about them below):

1. The git filter-repo tool (view source on GitHub).

2. The BFG Repo-Cleaner tool (it is open source – view source on GitHub).

After one of the previous options, there are additional steps to follow. Check the section Additional below.

If the goal is to remove a file that was added in the most recent unpushed commit, read the section Alternative below.

For future considerations, to prevent similar situations, check the For the Future section below.

Option 1

Using git filter-repo. Before moving forward, note that

If you run git filter-repo after stashing changes, you won’t be able to retrieve your changes with other stash commands. Before running git filter-repo, we recommend unstashing any changes you’ve made. To unstash the last set of changes you’ve stashed, run git stash show -p | git apply -R. For more information, see Git Tools – Stashing and Cleaning.

Let us now remove one file from the history of one’s repo and add it to .gitignore (to prevent re-committing it again).

Before moving forward, make sure that one has git filter-repo installed (read here how to install it), and that one has a local copy of one’s repo (if that is not the case, see here how to clone a repository).

1. Open GitBash and access the repository.

   cd YOUR-REPOSITORY
   

2. (Optional) Backup the .git/config file.

3. Run

   git filter-repo --invert-paths --path PATH-TO-YOUR-FILE-WITH-SENSITIVE-DATA
   

   replace PATH-TO-YOUR-FILE-WITH-SENSITIVE-DATA with the path to the file you want to remove, not just its filename to:

   • Force Git to process, but not check out the entire history of every branch and tag.

   • Remove the specified file (as well as empty commits generated as a result)

   • Remove some configs (such as remote URL stored in the .git/config file)

   • Overwrite one’s existing tags.

4. Add the file with sensitive data to .gitignore

   echo "YOUR-FILE-WITH-SENSITIVE-DATA" >> .gitignore
   
   git add .gitignore
   
   git commit -m "Add YOUR-FILE-WITH-SENSITIVE-DATA to .gitignore"
   

5. Check if everything was removed from one’s repository history, and that all branches are checked out. Only then move to the next step.

6. Force-push the local changes to overwrite your repository on GitHub.com, as well as all the branches you’ve pushed up. A force push is required to remove sensitive data from your commit history. Read the first note at the bottom of this answer for more details one this.

   git push origin --force --all
   

Option 2

Using BFG Repo-Cleaner. This is faster and simpler than git filter-branch.

For example, to remove one’s file with sensitive data and leave your latest commit untouched, run

bfg --delete-files YOUR-FILE-WITH-SENSITIVE-DATA

To replace all text listed in passwords.txt wherever it can be found in your repository’s history, run

bfg --replace-text passwords.txt

After the sensitive data is removed, one must force push one’s changes to GitHub.

git push --force

Additional

After using one of the options above:

1. Contact GitHub Support.

2. (If working with a team) Tell them to rebase, not merge, any branches they created off of one’s old (tainted) repository history. One merge commit could reintroduce some or all of the tainted history that one just went to the trouble of purging.

3. After some time has passed and you’re confident that one had no unintended side effects, one can force all objects in one’s local repository to be dereferenced and garbage collected with the following commands (using Git 1.8.5 or newer):

   git for-each-ref --format="delete %(refname)" refs/original | git update-ref --stdin
   
   git reflog expire --expire=now --all
   
   git gc --prune=now
   

Alternative

If the file was added with the most recent commit, and one has not pushed to GitHub.com, one can delete the file and amend the commit:

1. Open GitBash and access the repository.

   cd YOUR-REPOSITORY.l
   

2. To remove the file, enter git rm --cached:

   git rm --cached GIANT_FILE
   # Stage our giant file for removal, but leave it on disk
   

3. Commit this change using --amend -CHEAD:

   git commit --amend -CHEAD
   # Amend the previous commit with your change
   # Simply making a new commit won't work, as you need
   # to remove the file from the unpushed history as well
   

4. Push one’s commits to GitHub.com:

   git push
   # Push our rewritten, smaller commit
   

For the Future

In order to prevent sensitive data to be exposed, other good practices include:

• Use a visual program to commit the changes. There are various alternatives (such as GitHub Desktop, GitKraken, gitk, …) and it could be easier to track the changes.

• Avoid the catch-all commands git add . and git commit -a. Instead, use git add filename and git rm filename to individually stage files.

• Use git add --interactive to individually review and stage changes within each file.

• Use git diff --cached to review the changes that one has staged for commit. This is the exact diff that git commit will produce as long as one doesn’t use the -a flag.

• Generate Secret Keys in secure hardware (HSM boxes, hardware keys – like Yubikey / Solokey), that never leaves it.

• Train the team on x508.

Notes:

• When one force pushes, it rewrites the repository history, which removes sensitive data from the commit history. That may overwrite commits that other people have based their work on.

• For this answer one used content from some GitHub posts:

  • Removing sensitive data from a repository

  • About large files on GitHub

So, It looks something like this:

git rm --cached /config/deploy.rb
echo /config/deploy.rb >> .gitignore

Remove cache for tracked file from git and add that file to .gitignore list