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If a password, token, private key, or other personal data reached a remote Git repository, assume it has been copied. Revoke or rotate the credential with its issuer first, then rewrite every affected ref with git-filter-repo, force-push the cleaned refs, and coordinate cleanup of clones, forks, pull requests, and cached views. Deleting the file in a later commit does not remove the original data from history.
The safe sequence, in order
History cleanup and credential rotation solve different problems. Rewriting Git removes the data from the commit graph you control; it cannot invalidate a token that someone already downloaded. Treat the exposure as an incident and follow this order:
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- Contain the credential: revoke tokens, disable exposed passwords, and rotate API keys or private keys with the provider that issued them.
- Prepare a controlled rewrite: notify collaborators, pause writes, and work from a disposable fresh clone.
- Rewrite all relevant history: remove an entire path when a file is tainted, or replace known strings when the surrounding file must remain.
- Review the rewritten repository: inspect filter-repo reports and search every ref for the paths and strings.
- Publish the new graph: force-push rewritten refs, subject to branch-protection rules.
- Clean other copies and hosted remnants: have clone and fork owners remove old objects, and ask the host to purge cached views and sensitive pull-request references where its process permits.
- Prevent recurrence: move secrets out of tracked files, ignore local secret files, enable scanning, and document rotation steps.
Do not put the old secret in an incident ticket, chat message, issue, replacement file committed to the repository, or support request. Record identifiers such as the provider, affected repository, dates, and commit IDs instead.
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A normal deletion commit adds a new tree without the file, but earlier commits still point to blobs containing the password or personal data. Anyone with the old commit ID, an existing clone, a fork, a pull-request ref, an object cache, or a downloaded patch may still be able to retrieve it. A later revert has the same limitation: it changes the tip, not the historical objects.
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Rewriting history creates new commit IDs for the affected commits and descendants. The cleaned branch can look correct while old objects remain reachable elsewhere. That is why rotation is the first containment action and why a force-push alone is not a complete erasure plan.
Containment before touching Git
Revoke or rotate every exposed credential
Use the issuing service’s emergency or credential-management controls. Revoke access tokens, disable passwords, replace API keys, and generate new private keys. If a credential was embedded in automation, update the deployment or CI configuration at the same time so the replacement is actually used. Check for separate credentials in the same file or commit range; cleaning one value does not protect another exposed value.
Preserve an incident record without reproducing the secret. Useful fields include the repository and owner, affected branches or tags, first-known exposure commit, provider ticket number, rotation time, and people responsible for clone and fork cleanup.
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Pause writes and notify people who can publish refs
Tell maintainers and release automation not to push while the rewrite is being prepared. New commits created on the tainted graph make the set of refs harder to enumerate and can be reintroduced accidentally. Explain that the operation changes commit IDs and that old branches must not be merged back.
Prepare a disposable rewrite workspace
Use a fresh clone
Start outside any working directory that contains uncommitted work. A fresh clone gives git-filter-repo a complete, predictable object set and keeps your day-to-day checkout from becoming a second source of stale refs. Make a separate backup if your organization requires evidence retention, but protect that backup as sensitive material; it still contains the exposed data.
Inventory every place the data may exist
- Branches, including deleted or rarely used release branches.
- Annotated and lightweight tags.
- Pull-request or merge-request refs maintained by the hosting service.
- Renamed or moved paths; include the old names as well as the current path.
- Every spelling, encoding, line-ending variant, and formatting variant of a known string.
- Large-file storage objects and generated archives that may contain the same material.
List affected pull-request numbers before rewriting. The hosting service may need those numbers to remove special refs or cached diffs after the force-push.
Choose the rewrite method
| Situation | Method | What it changes | Main trade-off |
|---|---|---|---|
| An entire file is secret or contains inseparable personal data | Path deletion with --invert-paths --path |
Removes that path from every matched commit | All historical versions of the file disappear, including useful non-secret content |
| A file contains useful code plus a known password, token, or personal-data string | --replace-text |
Replaces matching text while retaining the rest of each file | Every variant must be identified; an unlisted representation can remain |
| The file moved or was renamed | Path deletion for each historical name, or replacements covering each name | Covers old and new paths in the rewritten graph | Missing an old name leaves an earlier copy intact |
| Only one branch appears affected | Usually rewrite all refs after inventory | Protects branches, tags, and other refs that may share the object | More commit IDs change and coordination becomes broader |
| Hosted copies, forks, or cached pull requests contain the object | Host-side purge requested after the local rewrite | Removes or hides service-managed references where the host approves it | It cannot clean clones or forks owned by other people |
git-filter-repo is the current GitHub-documented default for this work. BFG Repo-Cleaner is a documented alternative for file deletion or password replacement, but its commonly referenced guidance is older. Choose one tool for the rewrite and do not mix partially completed procedures.
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Rewrite an entire sensitive file with git-filter-repo
Remove the path from all matching commits
From the disposable fresh clone, replace PATH-TO-FILE with the repository-relative path:
git-filter-repo --sensitive-data-removal --invert-paths --path PATH-TO-FILEThis removes the path wherever it appears in the history processed by the tool. If the file was renamed, run the operation with every historical path, for example the old directory and the new directory, rather than assuming Git will infer every rename. A path containing spaces must be quoted for your shell.
Decide whether a path should be removed from the current checkout
If the file is still needed by the application, recreate it from a secure source after the rewrite, but do not commit the replacement containing live credentials. Prefer an environment-variable reference, a CI secret, or a managed secret injected at runtime. The rewrite is about removing historical content; it is not a substitute for changing how the application obtains configuration.
Replace known strings while keeping the file
Create a replacement list outside the repository
Make a temporary replacement file in a directory outside the clone and put each known sensitive value in the syntax accepted by your installed git-filter-repo. Keep this file out of Git and delete or securely dispose of it after the operation. Include old and new spellings, prefixes, URL-encoded forms, and test or production variants when they represent the same credential.
Run the replacement rewrite
git-filter-repo --sensitive-data-removal --replace-text ../passwords.txtThe relative path above assumes the replacement file is one directory above the repository. Adjust it to your workspace; the important property is that the file is not committed. Replacement text should be an unmistakable neutral marker, not a usable credential. Review the result for accidental changes to adjacent text, configuration syntax, checksums, or documentation examples.
When replacement is safer than deletion
Use targeted replacement when a source file contains valuable historical code and the sensitive value is a finite, known set of strings. Use whole-file deletion when the file contains mixed, unpredictable personal data, many secrets, or content you cannot confidently enumerate. If you cannot prove that every representation is known, deleting the path is the safer choice.
Understand what the rewrite changes
Commit IDs, signatures, and tags
Any commit whose tree or parent changes receives a new ID; descendants generally change as well. Signed commits and signed tags can no longer validate against the rewritten objects. Recreate signatures and release tags only after the cleaned graph has been reviewed, and tell consumers that old commit hashes are permanently obsolete for the project.
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Branches and tags are not independent safety zones
A secret introduced on one branch may be reachable from a tag or another branch. Inventory all refs before choosing a limited rewrite. A narrow ref selection can leave the same blob available through an unprocessed ref, so an all-ref rewrite is the normal choice unless you have documented proof that other refs are isolated.
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Review before publishing
Check filter-repo reports
git-filter-repo writes reports describing changed paths and first-changed commits. Read them rather than treating a successful exit status as proof of complete removal. Record the first-changed commit IDs for the hosting-service request and for your incident record.
Search every ref for paths and values
Search the rewritten refs, not only the default branch, for the removed path and for each sensitive string or variant. Inspect representative commits before and after the first change. Confirm that required source files, build metadata, and release notes still parse and that no replacement marker has broken syntax.
- Verify the sensitive file is absent from every relevant historical tree.
- Verify known values and their variants no longer appear in blobs, diffs, and tags you intend to publish.
- Check that the current working tree contains no live secret before pushing.
- Count the affected pull requests and note any special refs that require host assistance.
- Check large-file-storage reports if the repository uses LFS; an orphaned object may need separate handling.
Have a second maintainer review the inventory and search results. A reviewer should receive identifiers and findings, not a pasted copy of the secret.
Publish the cleaned refs
Force-push the mirror
When review is complete, push the rewritten refs:
git push --force --mirror originThis command updates all refs represented by the local mirror. Branch protection, signed-push requirements, or organization policy may reject it; obtain the required temporary administrative exception rather than weakening controls permanently. Confirm the remote URL and repository name before running a force push.
Expect pull-request refs to need separate handling
Hosting services often maintain pull-request refs and cached diffs outside the ordinary branch and tag namespace. A mirror push may not remove those service-managed objects. Use the host’s sensitive-data-removal process and provide the repository, affected pull-request numbers, first-changed commits from the filter-repo reports, and any orphaned LFS report requested by support.
Clean collaborators, forks, and other clones
Reclone when possible
The simplest reliable remedy for a collaborator is to delete the old local clone and clone the rewritten repository again. This removes stale local refs and unreachable objects more thoroughly than trying to repair an old working directory.
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Rebase work created from the old graph
If someone has unpublished work based on tainted history, they must rebase it onto the cleaned branch and resolve conflicts there. Do not merge an old branch into the cleaned repository: that can reintroduce the removed commits and their blobs. After a successful rebase, inspect the resulting diff for the sensitive path and values before publishing.
Handle forks and backups explicitly
Fork owners, mirrors, build caches, downloaded archives, and backup systems control their own copies. Send them the new starting commit and cleanup instructions, and ask them to delete or reclone old copies. A host cannot erase objects from a private clone it does not administer. If an old backup must be retained for legal or incident purposes, restrict access and prevent it from being restored as an active remote.
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After the force-push, contact the hosting service’s support process for sensitive data. Include:
- Repository owner and name.
- Paths and types of data removed, without reproducing the secret.
- Affected pull-request or merge-request numbers.
- The first-changed commit IDs reported by
git-filter-repo. - Details of any orphaned large-file-storage object.
- The time of credential revocation and the new repository tip.
Support may purge cached views and sensitive pull-request references when its criteria are met. Approval is not automatic, and the service’s process does not replace cleanup by fork and clone owners. Keep the support case number with the incident record.
Prevent the next leak
Store runtime secrets outside Git
Use environment variables or a dedicated secret-management service for passwords, API keys, signing keys, and personal data that applications need at runtime. Configuration files committed to Git should contain non-secret names or references, not live values. Rotate credentials on a schedule appropriate to their risk and immediately when exposure is suspected.
Ignore local secret files
Add local configuration filenames and generated credential files to .gitignore. This prevents accidental staging but is not a security boundary: an explicit git add -f can still track an ignored file. Pair ignore rules with review and scanning.
Scan before and after pushes
Enable the secret-scanning controls available from your Git host and development platform. Add pre-commit or CI checks for known token formats, private-key material, and organization-specific identifiers. Scanning should cover the working tree and history where supported, and alerts should trigger the same rotation runbook used for a confirmed leak.
Document an incident runbook
Write down provider contacts, revocation steps, repository-maintainer roles, the approved rewrite command, branch-protection exceptions, host-support requirements, and collaborator notification text. Practice the process with a harmless test value so the team knows who owns containment, rewriting, validation, and communication.
Common failure modes and recovery
“I deleted the file, but the secret still appears”
The deletion commit did not rewrite earlier objects. Revoke the credential if you have not already done so, identify every historical path, and run the path rewrite from a fresh clone. Then repeat the all-ref search and host-cleanup request.
“The command removed the new path but not the old one”
Include every name used before a rename or move. Review filter-repo path reports and search old release tags; a rename is not guaranteed to be represented identically in every historical commit.
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That clone still has the tainted graph. Stop the push, have the collaborator reclone or rebase onto the cleaned tip, and inspect the resulting refs. Do not merge the old branch to resolve the divergence.
“Force-push is rejected”
Branch protection or an administrative policy is blocking non-fast-forward updates. Coordinate a temporary, documented exception with repository administrators, keep the repository read-only during the window, and restore protections immediately after the mirror push.
“The secret is gone from branches but visible in a pull request”
Pull-request refs and cached diffs can be managed separately by the host. Provide the affected pull-request numbers and filter-repo first-changed commits to support; do not assume another force-push will remove those views.
“The credential cannot be rotated”
Escalate to the issuer and disable the account, integration, or key scope if possible. Limit permissions, monitor use, and treat the value as compromised permanently. History rewriting remains necessary for data minimization, but it cannot make an unrevokeable credential trustworthy again.
Quick Recap
Completion checklist
- The issuer has revoked, disabled, or rotated every exposed credential.
- Collaborators were notified and writes were paused during preparation.
- A fresh clone was used, with all branches, tags, pull-request refs, renames, and variants inventoried.
- The appropriate
git-filter-repopath deletion or text replacement completed. - Reports, historical trees, tags, diffs, and required code were reviewed.
- Rewritten refs were force-pushed under the repository’s approved controls.
- Collaborators and fork owners recloned or rebased without merging tainted branches.
- Host support received the repository, pull-request numbers, first-changed commits, and LFS details where applicable.
- Secrets now come from environment variables or a secret manager, local files are ignored, and scanning is enabled.
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