Skill references trigger unnecessary directory access prompts

### Describe the bug

When a skill includes bundled reference files (under ~/.copilot/skills//references/), Copilot CLI prompts the user for directory access confirmation for each reference file. This is disruptive because:

1. Skills are explicitly allowed to have references/ — these are bundled resources the skill depends on.
2. The user already trusted the skill by installing/enabling it.
3. The prompt fires repeatedly (e.g., "5 remaining"), breaking the agentic flow.

### Affected version

0.0.421

### Steps to reproduce the behavior

- Install a skill that has files in its references/ directory (e.g., work-awareness skill with references/meeting-radar.md).
- Invoke the skill.
- Observe repeated "Allow directory access" prompts for each reference file.

### Expected behavior

The `~/.copilot/skills//references/` directory should be automatically allowed when a skill is invoked. No user confirmation should be needed for skill-bundled reference files.

### Additional context

_No response_