Disabling extension-provided AI tools still leaves extension skills active for agent routing

[McCrille]

• Copilot Chat Extension Version: 0.43.0
• VS Code Version: 1.115.0
• OS Version: Windows
• Feature (e.g. agent/edit/ask mode): Agent mode, tool configuration, Chat Customizations
• Selected model (e.g. GPT 4.1, Claude 3.7 Sonnet): GPT-5.4
• Logs: Not attached. Reproducible from the UI without special setup.

Expected behavior:
Disabling an extension's AI tools should also disable that extension's skills for agent discovery and routing, or there should be a separate toggle for extension-contributed skills.

Actual behavior:
The extension's tools are disabled, but its skills remain active in Chat Customizations and can still influence agent routing. This leaves a mismatch where the agent can consider a skill whose related tools are unavailable.

Concrete example:
GitHub Pull Requests extension 0.134.0 is enabled for normal PR functionality. Its AI tools are disabled in the chat tools UI, but its PR-related skills remain active.

Steps to Reproduce:

1. Install an extension that contributes both AI tools and AI skills, for example GitHub Pull Requests.
2. Keep the extension enabled for its normal non-AI functionality.
3. In the agent tools configuration, disable the extension-provided AI tools.
4. Open Chat Customizations and inspect Skills.
5. Observe that the extension-contributed skills still appear active.
6. Send a prompt that matches one of those skills.
7. Observe that the agent can still consider the skill metadata even though the corresponding tools are unavailable.

Why this is a problem:
This creates a mismatch between discovery and execution. The extension still influences agent behavior after its AI tools have been disabled, and a skill-selected path can fail because the required tools are not available.