symlinkDirectories causes silent worktree cleanup failure

Description

When worktree.symlinkDirectories is configured in .claude/settings.json (e.g., to symlink node_modules), the automatic worktree cleanup on session exit silently fails because git worktree remove refuses to remove a worktree containing untracked files (the symlinks).

Steps to Reproduce

1. Configure worktree symlinks in .claude/settings.json:

``json
{
"worktree": {
"symlinkDirectories": ["node_modules"]
}
}
``

1. Start a session with --worktree
2. Make changes, commit, push, create PR
3. End the session / let it exit

Expected Behavior

The worktree should be cleaned up (or the user prompted) on session exit.

Actual Behavior

git worktree remove fails silently with:

fatal: '.' contains modified or untracked files, use --force to delete it

The symlinked node_modules directory is untracked, causing git worktree remove (without --force) to refuse. Worktrees accumulate over time.

Workaround

A WorktreeRemove hook that uses --force:

{
  "hooks": {
    "WorktreeRemove": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "jq -r '.tool_input.path // empty' | { read -r wt; [ -n \"$wt\" ] && git worktree remove --force \"$wt\" 2>/dev/null; git worktree prune 2>/dev/null; } || true"
          }
        ]
      }
    ]
  }
}

Suggested Fix

When symlinkDirectories is configured, the built-in worktree cleanup should either:

• Use --force (since the symlinks were created by Claude Code itself)
• Remove the symlinks before calling git worktree remove
• Recognize that symlinked directories are expected untracked content

Environment

• macOS Darwin 25.3.0
• Claude Code CLI
• pnpm monorepo with node_modules symlinked to avoid duplicating ~500MB per worktree