[BUG] [CRITICAL] Project Directory Deletion during background task conversion with Sonnet 4.6 1mln context

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?

 │ 18:55:37            │ Sonnet 4.6 submits rm -rf command (foreground, NOT requesting background)                               │
  ├─────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────┤
  │ 18:55:40            │ Claude Code auto-promotes command to background task bv29bchzl                                          │
  ├─────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────┤
  │ 18:55:40 – 18:57:36 │ 119 seconds of execution with zero output (117 progress entries)                                        │
  ├─────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────┤
  │ 18:57:37            │ Background task completes (exit code 0, output file: 0 bytes)                                           │
  ├─────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────┤
  │ 18:57:37+           │ Every subsequent command fails: "Working directory sera no longer exists"  

What Should Happen?

Claude should be careful with deleting entire project directories

Error Messages/Logs

Most Likely Root Cause

A bug in Claude Code v2.1.59's auto-background-promotion mechanism for bash commands. When the rm -rf command was automatically promoted from foreground to background execution, something in the path handling went wrong

 The circumstantial evidence is strong:
  - The previous session ran the same pattern (rm + df) in foreground → no issue
  - This session's command was auto-promoted to background → entire directory deleted
  - The execution duration matches deleting ~120GB, not 463MB

Steps to Reproduce

something like this:

collect the remaining my_config_v2 config batch #3 run from new vm and transfer to the local directory with the same structure as previous batches

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

v2.1.59

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Warp

Additional Information

_No response_