Agent gets confused when shell tool points at directory it removes

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1

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

My workflow makes heavy use of git worktrees and when the agent cleans up the worktree (like moving the worktree to the main checkout for testing) many times it gets confused because it was using the shell tool at the worktree location and after deleting the directory it tries to use the shell but forgets it’s pointed at the deleted worktree.

it says things like:

“The shell is unresponsive right now — commands are running but not returning. Would you be able to open a fresh terminal and run this yourself?”

and I can (now that I finally figured out what it keeps doing wrong) easily point it in the right direction:

“use a proper CWD in your shell” is all it takes for it to realise it’s mistake and get it on track.

the bug is this: your shell tool, when called with a CWD that deson’t exist, needs to not silently fail, and instead it should hint to the LLM that the CWD does not exist, so that it can auto correct its mistake.

Steps to Reproduce

have the agent create a branched worktree tracking a branch
have the agent run some shell commands in there like run a test or whatever.
have the agent move the worktree and mnove the branch back to main checkout
Have the agent run a shell command again (it will likely forget to use the new CWD)

Expected Behavior

the agent is told by the harness that the CWD used in the shell tool does not exist and it automaticallyu corrects itself.

Screenshots / Screen Recordings

Screenshot 2026-07-14 at 2.38.06 PM.png
Screenshot 2026-07-14 at 2.38.06 PM.png801×422 36.9 KB

Operating System

MacOS

Version Information

Version: 3.8.23
VS Code Extension API: 1.105.1
Commit: 7cf19b7482706625cdb70db3211b7dd035b7aa30
Date: 2026-06-23T14:57:42.334Z
Layout: glass
Build Type: Stable
Release Track: Default
Electron: 40.10.3
Chromium: 144.0.7559.236
Node.js: 24.15.0
V8: 14.4.258.32-electron.0
xterm.js: 6.1.0-beta.256
OS: Darwin arm64 25.3.0

For AI issues: which model did you use?

Claude Sonnet 4.6 Medium

Does this stop you from using Cursor

No - Cursor works, but with this issue

6

Hey Keith!
This is a bug on our side, and one we’ve had reported before: when the agent’s shell holds a working directory that’s since been moved or deleted (like a cleaned-up worktree), the command fails silently or hangs instead of signaling the directory is gone, so the agent gets confused and asks you to run things manually.

Your workaround is the right one. The two reliable options:

  1. Tell the agent to use a valid working directory (what you found).
  2. Start a fresh terminal, or point it back at your main checkout after moving/deleting a worktree, which resets the stale directory.

And you’ve nailed the ideal fix: the shell tool should give the model a clear “that directory no longer exists” signal so it auto-corrects. I’ve flagged your report to the team.