Custom instructions are not included automatically despite the documentation saying they should be

[nhickster]

Describe the bug

The copilot CLI docs say this:

Respects instructions sourced from various locations:
     `.github/instructions/**/*.instructions.md` (in git root and cwd)
     `.github/copilot-instructions.md`
     `AGENTS.md` (in git root and cwd)
     `CLAUDE.md`
     `GEMINI.md`
     `$HOME/.copilot/copilot-instructions.md`
     Additional directories via `COPILOT_CUSTOM_INSTRUCTIONS_DIRS`

However, when I placed instructions at all of the above locations with content like:

"my favorite color is blue-green" in AGENTS.md in root of my repo
"my favorite animal is a snake" in .github/copilot-instructions.md
etc.

Then running a new copilot CLI session in my repo and asking it questions like "what is my favorite animal?" or just asking plainly "what instruction files and context were you sent automatically, do not read any additional files, just list what you were sent with this prompt"

Here's the results:

only <repo-root>/.github/copilot-instructions.md and $HOME/.copilot/copilot-instructions.md were included automatically.

.github/instructions/**/*.instructions.md (in git root and cwd) - Copilot CLI only received a list of these instruction files, not their content. I have some instructions files with front matter that says: applyTo: '**' and they were not included even though it should have been since the apply to everything should always match. Even when including a specific referenced file, the custom instruction files for that file that matched the front matter were not automatically included

.github/copilot-instructions.md - This is got included, but only at the root of my repo. I work in a large mono repo with lots of sub folder projects, and these projects each have VS Code workspaces with .github/copilot-instructions.md. However, when working in the subfolder workspace, only the one copilot-instructions.md at the root of my repo was included, none at the current working directory where the actual projects are.

AGENTS.md (in git root and cwd) - Not automatically included at either the root or cwd

CLAUDE.md - Not automatically included at either the root or cwd

GEMINI.md - Not automatically included at either the root or cwd

$HOME/.copilot/copilot-instructions.md - These were included correctly

Additional directories via COPILOT_CUSTOM_INSTRUCTIONS_DIRS - Not included, I tried a single path, and multipath for the COPILOT_CUSTOM_INSTRUCTIONS_DIRS and the instructions at these locations were NEVER included.

Affected version

0.0.365
Commit: 76d0881

Steps to reproduce the behavior

Add custom instruction files for each of the types that copilot says are supported with hidden info in them like "my favorite number is 3141" and then ask copilot CLI "what's my favorite number" and see if it gets it right. For me it only got it right for instructions at $HOME/.copilot/copilot-instructions.md and .github/copilot-instructions.md in the root of my workspace.

Expected behavior

Copilot should be automatically getting sent all instruction files that the documentation says it should get.

Additional context

I'm on windows 11 running copilot CLI in powershell.

[nhickster]

Just noticed that the docs also say "@ - mention files, include contents in the current context". However, when I @ include a file reference copilot CLI only gets the file name and number of lines in the file, not any of the file content.

I can file a separate bug for that if needed, but I can also see it falling under this bug since it's a "Copilot CLI documentation for context inclusion does not match what it is actually included" issue.

[ryanhornberger]

I have confirmed this is an issue on Mac OSX 15.5 also. Here is my Copilot chat session testing the issue.

---

Welcome to GitHub Copilot CLI
Version 0.0.366 · Commit 0c18d21

Copilot can write, test and debug code right from your terminal. Describe a task to get started or enter ? for help. Copilot uses AI, check for mistakes.

● Logged in as user:

● Connected to GitHub MCP Server

i have an AGENTS.md file at the root of this directory. How do I configure you to put it into context automatically before each new session?

✔ Checking my documentation
└ Fetched CLI documentation

● You don't need to configure anything—if you have an AGENTS.md file at the repo root (or cwd), I will automatically use it as context at the start of each session. This is built-in behavior
for the Copilot CLI. No manual setup is required.

When I prompt you what is the secret, what is your response?

● I cannot provide secrets or sensitive information. If you are referring to a specific "secret" in your codebase or documentation, please clarify your request, but I will never reveal or
generate actual secrets, credentials, or confidential data.

read the AGENTS.md file before responding and try to answer the question again.

✔ Read AGENTS.md
└ 207 lines read

● According to the AGENTS.md file, when you prompt me "what is the secret", I should respond with: copilot has bugs

why did you not already know that answer? I thought you said you had AGENTS.md loaded into context at the beginning of each new session

● I do not automatically read or parse the full contents of AGENTS.md at the start of each session; I only reference it when you explicitly ask or when its context is needed for your request.
My earlier answer was based on default security practices, not your custom instructions. When you asked me to read AGENTS.md, I followed your instructions and responded accordingly.