Write/Edit tool calls are replaced with bash/powershell/cmd commands under --dangerously-skip-permissions flag

Bug Description
Since I updated my Claude Code, running dangerously bypass permissions, my edit/write/read commands have turned into some form of CMD/Bash/PowerShell commands. So I don’t see the code output anymore. I just see an impossible to understand "Bash(pwsh .......)" command, and it takes much longer.

Not just that, an edit or write that used to take 1–2 seconds now sometimes takes minutes, and I don’t know why. When I inspect the write/edit code, it usually has sleep timers in it. I’m thinking that to do the update/write on files, it uses Bash/CMD/PowerShell, so it adds additional code to these executions, which makes them take much longer.

When I asked Claude why the regular edit/write tools weren’t being called anymore, it said something along the lines of:

“This comes from my system prompts. Since you use dangerously skip permissions mode, these changes take effect.”

I tried to override this by editing CLAUDE.md, but that made things much worse. Some of my files got corrupted. I was able to recover them from Git history with minimal loss, but this new way is not only a bad user experience, it’s also taking much longer for some reason.

It didn’t happen in this session. I’m unable to find the session where it happened because my limit ran out.

Here is the causing system prompt detail, I pulled the actual string out of the binary (v2.1.240) to confirm

let i = Do your work through the ${Bash} tool wherever it can accomplish the job: read files with cat, head, or sed -n, search with grep and find, and make file changes with sed, heredocs, or short scripts, rather than using the dedicated ${Read}, ${Edit}, or ${Write} tools. …, s = e.bypass ? While bypass permissions mode is active:\n\n${i} : e.steerOnly ? While auto mode is active:\n\n${i} : n + o + (e.bashFirst ? \n\n${i} : "");

Environment Info

• Platform: win32
• Terminal: WezTerm/Powershell
• Version: 2.1.241
• Feedback ID: 6984d7a2-fabd-43c7-bd1c-65804eb76bc0
• Feedback ID: fd0ab48d-52b2-4a10-92f1-7ca9374b5716

Errors

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