[BUG] Claude Code always asks for permission

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?

I'm using Claude Code app (linux - Claude 2.37337.1) and Claude Code CLI (v2.1.300) and in both is not possible to make the agents work while AFK.

I tried with different permissions mode, auto, skip permissions and accept editions but it always asks for permissions to run the commands.

Every time I ask them to work on an issue every command needs to be accepted. For example it needs to read an issue from GitHub, the command it wants to run is this one:

git fetch origin && git worktree add -b feat/issue-35 .claude/worktrees/issue-35 origin/main && cd .claude/worktrees/issue-35 && git log --oneline -1 && ls && ls server/src docs docs/adr

Then it needs permission to execute this command:

cat CONTEXT.md | head -80; wc -l server/src/*.rs server/tests/* 2>/dev/null; cat server/Cargo.toml

When it wants to modify a file it uses commands like echo, sed or python.

What Should Happen?

Any agent should make permission to create or modify code and it should use its own tools for reading and writing.

Error Messages/Logs

Steps to Reproduce

Start a coding session from Claude Code Desktop for linux or Claude Code CLI and ask to perform any task, the agent will ask for everything.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.300

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

_No response_