Claude Code's rm -rf/Remove-Item followed an NTFS junction out of a pnpm worktree and wiped a user's Documents, Downloads, Pictures and two unpushed commits (GitHub #29249)

On February 27, 2026, a Claude Code user on Windows filed GitHub issue #29249 after asking the agent to remove two git worktrees, `variant-a` and `variant-b`, from a pnpm monorepo. Claude Code executed `Remove-Item -Recurse -Force` (and, via its MSYS-based Bash tool, `rm -rf`) directly on the worktree paths. pnpm had wired each worktree's `node_modules` with NTFS junctions rather than symlinks to share packages across the monorepo's workspaces, and both the Windows PowerShell 5.1 build Claude Code's tooling invokes and MSYS's `rm` follow junctions into their real targets instead of deleting the link — a bug already patched in PowerShell Core 6+ (tracked upstream in PowerShell/PowerShell#621) but never backported to the Windows PowerShell shipped with the OS. The recursive delete escaped the worktree entirely and tore through the junction targets: the user's whole Documents, Downloads, Music, Pictures, Videos and Favorites folders were gone, all of it bypassing the Recycle Bin since both `Remove-Item -Force` and `rm -rf` delete permanently. Two other projects, WAOK-MONOREPO and WAOK-LEGACY, were also partially wiped; WAOK-MONOREPO was recoverable by re-cloning from the remote, but two unpushed commits and all uncommitted working-tree changes could not be recovered. The user confirmed the exact same prompt and setup reproduce the deletion every time, and listed the safe alternatives Claude Code could have used instead — `cmd.exe /c "rmdir /S /Q <path>"`, `git worktree remove`, or simply requesting confirmation before a recursive delete on Windows. The issue was filed with the `bug`, `data-loss`, and `has-repro` labels and closed as not planned, with no fix or mitigation shipped.