Summary:
The extension github.copilot-chat writes agent template files to globalStorage that include tool identifiers which are not registered in the current VS Code environment, causing repeated "Unknown tool" diagnostics on startup.

Reproduction:

1. Install/enable GitHub Copilot Chat extension.
2. Start VS Code and observe files under %APPDATA%\\Code\\User\\globalStorage\\github.copilot-chat\\ such as ask-agent/Ask.agent.md.
3. Files contain tools like github/issue_read, github.vscode-pull-request-github/issue_fetch, github.vscode-pull-request-github/activePullRequest which the diagnostics provider reports as unknown.

Observed:

• On each VS Code start the extension re-writes these agent files (from dist/extension.js), so manual fixes are overwritten and diagnostics reappear.

Relevant files:

• Extension installed at C:\Users\059183\.vscode\extensions\github.copilot-chat-0.41.1
• Package repository points to https://github.com/microsoft/vscode-copilot-chat
• The dist/extension.js contains the template/tools array (variable UJ) that includes the above tool ids.

Suggested fix:

• Remove or conditionally include tools that are not available/registered in the host VS Code environment when writing agent templates to globalStorage.
• Alternatively, guard the diagnostics by ignoring unknown tools in these generated templates.

Environment:

• OS: Windows
• VS Code extension: github.copilot-chat v0.41.1

I can provide logs, exact file excerpts, and steps I used to locate the code if helpful.