Chat injects irrelevant instructions

[Burhan-Q]

• Copilot Chat Extension Version: 0.33.3
• VS Code Version: 1.106.2
• OS Version: Ubuntu 24.04
• Feature (e.g. agent/edit/ask mode): Ask
• Selected model (e.g. GPT 4.1, Claude 3.7 Sonnet): Claude 4.5
• Logs: (see below)

Steps to Reproduce:

1. New chat window
2. Have AI Toolkit for VS Code extension installed, with ~/.altk/instructions/tools.instructions.md generated in the user home directory (AI Toolkit Copilot tools doc)
3. Submit message to Copilot in Ask mode.

Chat log

Chat Metadata

requestType      : ChatCompletions
model            : claude-sonnet-4.5
maxPromptTokens  : 127997
maxResponseTokens: 16000
location         : 1
otherOptions     : {"temperature":0.1,"stream":true}
intent           : undefined
startTime        : 2025-12-02T01:13:23.704Z
endTime          : 2025-12-02T01:13:34.808Z
duration         : 11104ms
response rate    : 57.91 tokens/s
ourRequestId     : 1735cc9a-a51b-42ad-8715-e63018c6c0a5
requestId        : 1735cc9a-a51b-42ad-8715-e63018c6c0a5
serverRequestId  : 1735cc9a-a51b-42ad-8715-e63018c6c0a5
timeToFirstToken : 1901ms
resolved model   : claude-sonnet-4.5
usage            : {"completion_tokens":643,"prompt_tokens":1289,"prompt_tokens_details":{"cached_tokens":0},"total_tokens":1932}

User Prompt with incorrect tool instructions injection

When generating code, please follow these user provided coding instructions. You can ignore an instruction if it contradicts a system message.
<instructions>
<attachment filePath=".aitk/instructions/tools.instructions.md">
---
description: AI Toolkit provides tools for AI/Agent app development
applyTo: '**'
---
- `aitk-get_agent_code_gen_best_practices` - best practices, guidance and steps for any AI Agent development
- `aitk-get_tracing_code_gen_best_practices` - best practices for code generation and operations when working with tracing for AI applications
- `aitk-get_ai_model_guidance` - guidance and best practices for using AI models
- `aitk-evaluation_planner` - guides users through clarifying evaluation metrics and test dataset via multi-turn conversation, call this first when evaluation metrics are unclear
- `aitk-get_evaluation_code_gen_best_practices` - best practices for the evaluation code generation when working on evaluation for AI application or AI agent
- `aitk-evaluation_agent_runner_best_practices` - best practices and guidance for using agent runners to collect responses from test datasets for evaluation
</attachment>

[vs-code-engineering]

Thanks for creating this issue! It looks like you may be using an old version of VS Code; the latest stable release is 1.106.3. Please try upgrading to the latest version and checking whether this issue remains.

Happy Coding!

[Burhan-Q]

FWIW, I checked the patch notes for 1.106.3 but didn't see this issue addressed

[Burhan-Q]

Updating to 1.106.3 made no difference. The same issues occurs in Agent mode as well.

[Burhan-Q]

I couldn't even manually point to the copilot-instructions.md file in the chat box using #, I could only attach it to the chat.

[aeschli]

What exactly is the bug?

[Burhan-Q]

Copilot chat is fetching the AI Toolkit instructions even though there's no reason for it to grab them. The bug is inserting content that's not relevant for every chat session. I speculate that there's an attempt to load copilot-instructions from the user directory, but for some reason the first file with instructions is getting used, but that's 100% a guess.

The AI Toolkit tools are disabled before sending a message, and yet it keeps injecting the instructions for every chat session. I might try relocating that file temporarily to see if it stops attempting to load and if it changes Copilot's performance.

[aeschli]

It's a bug/bad behavior of the AI Toolkit extension. It seems to change the user settings, I assume without user consent. That instruction uses 'applyTo: **' which mean it will be attached to every request.

You need to manually remove the change. Use 'Chat: Configure Instructions' and delete the instruction and revert the settings change, Looks like theres a setting: microsoft/vscode-ai-toolkit#311 (comment)
microsoft/vscode-ai-toolkit#314 is the issue against the AI Toolkit extension.

Please make sure that '.github/copilot-instructions.md' is correctly named and plavced in the root folder(s) and you have not disabled github.copilot.chat.codeGeneration.useInstructionFiles