[BUG] ClaudeCode Opus 4.6 not respecting permissions

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?

Claude is not respecting permissions.

I have this in my repo's .claude/settings.json:

{
  "permissions": {
    "allow": [
      "Bash(python3*)",
      "Bash(curl*)",
      "Bash(cd *)",
      "Bash(pnpm *)",
      "Bash(mkdir*)",
      "Bash(ls*)",
      "Bash(cat*)",
      "Bash(find*)",
      "Bash(wc*)",
      "Bash(echo*)",
      "Bash(cp*)",
      "Bash(mv*)",
      "Bash(touch*)",
      "Bash(head*)",
      "Bash(tail*)",
      "Bash(grep*)",
      "Bash(sort*)",
      "Bash(uniq*)",
      "Bash(sed*)",
      "Bash(awk*)",
      "Bash(git *)",
      "Bash(node*)",
      "Bash(npx*)",
      "Bash(which*)",
      "Bash(pwd*)",
      "Bash(diff*)",
      "Bash(test*)",
      "Bash(for *)",
      "Bash(if *)",
      "Bash(while *)",
      "Bash([*)",
      "Bash(true*)",
      "Bash(false*)"
    ],
    "deny": [
      "Bash(rm *)",
      "Bash(rm -*)",
      "Bash(rmdir*)"
    ]
  },
  "mcpServers": {
    "wikipedia": {
      "command": "node",
      "args": ["task/mcp/wikipedia/index.js"]
    }
  }
}

Literally just now, asked me:

Bash(mkdir -p somepath)

Especially it keeps asking for loops and random inline long nested bash scripts.

Like this:

for lang in danish norwegian-bokmal; do echo "$lang"; done

Why is it not respecting my settings.json? I restarted claude command several times.

What Should Happen?

It should not run these random for, while, if nested bash commands ever, I am trying to tell it not to, but it is not respecting them.

Error Messages/Logs

Steps to Reproduce

Not sure, just ask it to do a lot of stuff.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.39 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

Opus 4.6