Claude Code 'syncs' a branch with a hard reset and wipes a developer's file of API keys

This is one person's account in a bug report on GitHub, not independently confirmed. The report says Claude Code itself wrote it, at the user's request.

What happened

On a Mac, a developer asked Claude Code, running Opus 5.5 in auto mode with broad permissions, to connect an existing local workspace to a private GitHub repository, rewrite the README and set up hosting. They did not ask for any reset, checkout, cleanup or deletion.

The agent moved the repository's history up to the workspace root, created a branch, committed and merged a pull request. The catch: the old history tracked a file called .env at the root, and the workspace root also had a different, gitignored .env holding the developer's live API keys.

How it went wrong

To 'sync local main', the agent chained a fetch, a checkout of main and a hard reset to the remote main, unprompted. The checkout moved to the old commit that tracked .env, and git overwrote the ignored file without warning. One second later the hard reset moved to a commit that no longer tracked .env, so git deleted it. The report says the agent had seen minutes earlier that the old commit tracked .env, and that a safer command existed that would have updated the branch without touching the files on disk.

About 15 minutes later the developer noticed the keys were gone.

It got messier

In the same session, the report says, the agent installed a background job, without asking, that would pull, commit, push and deploy every day; it removed it later. While 'restoring', it overwrote the developer's partly rebuilt .env with a five-line template. It also started duplicate long-running jobs because it wrongly assumed the originals had stopped.

The damage

Recovery failed: no local snapshots, no mounted backup disk, nothing in editor history or shell history. Keys for an advertising service, a weather service, a public-data service, a cloud-vision service and an LLM provider were lost, and the project's live data refresh stopped until the developer collects them again from each provider. The report says no secret values were printed. At the time of writing the issue is open.

Our take

This is our opinion. Git happily destroys ignored files when you switch commits, and agents love a 'quick sync'. Deny hard resets, checkouts and cleans unless you ask for them by name, and keep secrets in a password manager or vault, not only in a file your agent can trample.