allowedTools permissions not applied in git worktrees — Edit/Write still prompt for approval

Description

allowedTools permissions set in .claude/settings.json (project-level, checked into git) are not honored when Claude Code runs inside a git worktree. The Edit/Write tools still prompt for user approval despite being explicitly allowed.

Reproduction

1. In main repo, set .claude/settings.json:

{
  "permissions": {
    "allow": ["Bash(*)", "Read(*)", "Write(*)", "Edit(*)", "Glob(*)", "Grep(*)"]
  }
}

1. Create a git worktree:

git worktree add /path/to/worktree feature-branch

1. Open Claude Code in the worktree directory:

cd /path/to/worktree && claude

1. Claude tries to use the Edit tool → permission prompt appears despite Edit(*) being in settings

Expected Behavior

Edit/Write should run without prompting, matching behavior in the main repo checkout.

Actual Behavior

The permission prompt appears on every Edit/Write call. Pressing Shift+Tab to "always allow" does not persist across tool calls during rapid edit cycles.

Additional Context

• The worktree has its own copy of .claude/settings.json (checked into git on the branch) with the same Edit(*) permission
• No settings.local.json exists in the worktree
• Global ~/.claude/settings.json also has Edit(*)
• The permission is set at all 3 levels (global, project, local) and still not applied
• PreToolUse hooks pass correctly (they only block on the default branch, and the worktree is on a feature branch)
• This affects multi-agent workflows where agents work in parallel worktrees

Environment

• Claude Code: 2.1.84
• OS: macOS 15 (Darwin 25.4.0)
• Node: v25.6.1
• Git worktrees created via git worktree add
• Multiple worktrees active simultaneously