[BUG] Claude not using same settings across worktrees of the same repo

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 using settings from the project/repository root directory in worktrees of that repository.

❯ run linting on the whole project

⏺ Bash(lint)
  ⎿  Running…

────────────────────────────────────
 Bash command

   lint
   Run linting

 This command requires approval

 Do you want to proceed?
 ❯ 1. Yes
   2. Yes, and don’t ask again for: docker compose:*
   3. No

 Esc to cancel · Tab to amend · ctrl+e to explain
────────────────────────────────────

⏺ Bash(lint)
  ⎿  Interrupted · What should Claude do instead?

❯ check ../mainbranch/.claude/settings.local.json and tell me why did you have to ask for permission to run this command? it should be in the allowed part of the settings

⏺ Read 1 file (ctrl+o to expand)

⏺ The settings are in /Users/me/Projects/thisproject/mainbranch/.claude/settings.local.json, but we're working in /Users/me/Projects/thisproject/featurebranch/. This is a
  different repo/directory, so those settings don't apply here. The featurebranch project needs its own .claude/settings.local.json with the same allow rules.

  Want me to create one for this repo?

What Should Happen?

Claude should use settings from the project main directory.

Error Messages/Logs

Steps to Reproduce

Just make a worktree git worktree add ../featurebranch featurebranch and work in it, claude will ignore anything that was in .claude of the main directory

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.66 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_