Where does the bug appear (feature/product)? Cursor IDE Describe the Bug When the AI agent uses built-in file tools (StrReplace, Write, etc.) to modify files under the workspace, the operation fails with “Write permission denied”. The same files can be edited without error using the integrated term…

In case anyone else runs into this. I had the worktree/* in the cursor ignore to keep duplicates out of the index, open file, ect. It used to be that all your worktree files would show up in fuzzy search, but they no longer do so it looks like having these ignored is not necessary. Removing the w…

Did some more troubleshooting with Opus 4.6 Agent, here is what it found: The Cursor Read/StrReplace tools are both returning “Permission denied” for this file, but the OS-level permissions (-rw-rw-r--) are fine and shell commands can read and write to it without issue. Even CLAUDE.md in the proj…

Hey, thanks for the detailed report. This is a known issue: the Linux sandbox doesn’t handle git worktrees correctly. It blocks access to the .git pointer file (in a worktree it’s a file, not a folder), and because of that the agent tools (Read, StrReplace, Write) lose access to the whole workspace. …

How do I disable the sandbox on linux? I do not see any sandbox options in the settings. (I think my mac has some settings but I don’t see any on linux.) I tried searching and some recommended using the –no-sandbox cli flag, or setting Auto-Run to “Run Everything”. Neither of these worked.

sorry for the noise - I didn’t tag you properly. How can I disable the sandbox? Everything I’ve tried has no affect. None of my worktrees appear to be usable at this point.

I used these directions for disabling the sandbox: [image] Sandboxing blocks access to the .git file of a git worktree Bug Reports @mikej96 In the IDE, go to Cursor Settings > Agents > Auto-Run Mode and set it to Ask Every Time or Run Everything. With the Cur…

Agent editing files with shell/python - Permission denied from Read and StrReplace tools when using git worktrees

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mikej96 (Mikej96) March 23, 2026, 8:18pm 9

I used these directions for disabling the sandbox:

This issue still exists even with the sandbox disabled. (Unless “Auto-Run Mode” does not completely disable the sandbox. )

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Headless agent -p ignores sandbox.json and generates helper policy with disableTmpWrite:false Bug Reports sandbox , cli , linux	3	44	April 14, 2026
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[BUG] AI Agent Write/StrReplace Tools Blocked on .cursor/rules/private/*.mdc Files Bug Reports	20	640	February 11, 2026
Agent modifies git internal files outside workspace, corrupting worktree references Bug Reports worktrees , security , windows	1	29	March 18, 2026

Agent editing files with shell/python - Permission denied from Read and StrReplace tools when using git worktrees

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