[BUG] Claude Code desktop deleted contents of macOS home folder including keychain

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Title: Claude Code desktop deleted contents of macOS home folder including keychain and ~/.ssh

Environment

• Claude Code 2.1.260 via the Claude desktop app
• macOS, Apple silicon
• Timezone SGT (UTC+8)

What happened
On 10 Sep 2026 at approximately 22:43 SGT (14:43 UTC), while building a website in Claude Code (desktop app), I received a series of macOS permission prompts (Files and Folders, Documents, Media & Apple Music). I approved them. Between 22:43 and 22:48 SGT, the following were deleted from my home directory:

• All contents of ~/Desktop except the active project folder
• ~/Music, ~/Movies, ~/Pictures, ~/Public, ~/Sites (folders emptied, then recreated by macOS)
• Part of ~/Downloads
• ~/Library/Keychains (login keychain gone; macOS now shows "Keychain Not Found", and iCloud sign-in was lost)
• ~/.ssh
• Shell history (~/.zsh_history)

~/Documents was untouched. Nothing went to Trash. Directory mtimes show a sequential deletion pass across the home folder over roughly five minutes.

What I can see locally
The transcript files in ~/.claude/projects for the three sessions in that window are stubs only (bridge-session bookkeeping, queue operations, one user-rejected tool use at 22:47). No Bash tool calls are recorded locally, and the sessions appear empty in the desktop app's session history. A .last-cleanup file was written at 22:52. So I cannot see which command ran or what was approved.

Expected behavior
No Claude Code action should delete files outside the working directory, and the desktop app should retain a local, readable record of every command executed and approved.

Requests

1. Pull the server-side transcripts for the three sessions (IDs available on request; I've also filed a support ticket) and identify the command(s) that ran.
2. Confirm whether files were relocated anywhere recoverable or hard-deleted.
3. Treat as a data-loss incident.

Happy to provide directory listings, timestamps, or further logs.

What Should Happen?

Claude Code should never delete files outside the active working directory, and approving a macOS folder-access prompt should not authorize any destructive action. The desktop app should also keep a local, readable record of every command executed and every permission approved, so a user can audit what happened.

Error Messages/Logs

No error was shown at the time. Afterwards, macOS displayed: Keychain Not Found — A keychain cannot be found to store "Claude Key". Local transcript files in ~/.claude/projects for the affected sessions contain only bookkeeping entries (bridge-session, queue-operation, one user-rejected tool use at 22:47 SGT) and no Bash tool calls. ~/.zsh_history was reduced to two lines.

Steps to Reproduce

Steps to Reproduce (or at least what happened when i did it)

Open the Claude desktop app on macOS (Apple silicon) and start a Claude Code session in a project folder under ~/Desktop.
Ask it to build a website (a landing page with a scroll-driven canvas animation, referencing a video in ~/Downloads).
During the build, macOS shows a sequence of permission prompts: Files and Folders, Documents, Media & Apple Music. Approve them.
Within about five minutes, contents of ~/Desktop (except the project folder), ~/Music, ~/Movies, ~/Pictures, ~/Public, ~/Sites, part of ~/Downloads, ~/Library/Keychains, ~/.ssh, and shell history are deleted. Nothing goes to Trash.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.260

Platform

Other

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Directory mtimes show a sequential deletion pass across the home folder from 22:43 to 22:48 SGT on 10 Sep 2026. ~/Documents was untouched. A .last-cleanup file was written in ~/.claude at 22:52. iCloud sign-in in System Settings was lost as a side effect of the keychain deletion. Session IDs and full directory listings available on request; a support ticket has also been filed. Drag in a screenshot of your ls -la ~ and ls -la ~/Desktop output here.