Agent templates write unknown tools into globalStorage causing diagnostics

[Hayvey]

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.

[wrayste]

I can confirm this on Linux as well with GitHub Copilot Chat 0.41.1.

What I’m seeing:

• On startup, Copilot Chat generates built-in agent files under user globalStorage such as ask-agent/Ask.agent.md.
• The generated tools list includes stale/unsupported tool ids, specifically github/issue_read.
• The prompt diagnostics provider then reports Unknown tool 'github/issue_read'.
• Manual edits to the generated file are not durable because the extension rewrites the file.

This looks like an extension bug rather than a user/workspace customization issue. I traced it back to the extension bundle, where the generated Ask agent config is built from hard-coded tool arrays in dist/extension.js and those arrays still include github/issue_read.

Expected:

• Generated built-in agent templates should only contain tool ids that are actually registered in the current host environment.

Suggested fix:

1. Remove github/issue_read from the built-in generated agent tool lists.
2. Prefer deriving the generated tool list from the currently registered/available tools instead of hard-coding stale ids.
3. As a defensive fallback, either skip unknown tools when generating these files or suppress unknown-tool diagnostics for extension-generated agent files under globalStorage.

Repro:

1. Install/enable GitHub Copilot Chat 0.41.1.
2. Start VS Code.
3. Open the generated Ask agent file under Copilot Chat globalStorage.
4. Observe github/issue_read in the frontmatter.
5. Observe the Unknown tool 'github/issue_read' diagnostic.

Environment:

• OS: Linux
• Extension: GitHub Copilot Chat 0.41.1

[imasubmarine]

I can confirm this on Windows with GitHub Copilot Chat 0.41.1.
It appeared as soon as i updated to VS Code 1.113

[arthurbcd]

I can also confirm this, any ETA for this?

[omagoduck]

I also confirm.

[osric-ukho]

Here too, quite irritating.

Version: 1.113.0 (system setup)
Commit: cfbea10c5ffb233ea9177d34726e6056e89913dc
OS: Windows_NT x64 10.0.19045
GitHub Copilot Chat extension: 0.41.1