Agents.md instruction files ignored/not used when copilot-instructions.md is present

[rasidr]

Describe the bug

Copilot CLI (v0.0.353) applies copilot-instructions.md but appears to ignore agents.md file, despite the help text listing agents.md as a supported instruction file.

Behavior difference:

• In Copilot CLI: responses only include the tag from copilot-instructions.md.
• In VS Code (same repo): responses include both tags (from copilot-instructions.md and agents.md).

It would also be nice to have a way to see which instruction files are actually used in a session, like VS Code shows Used x references. (Possibly related to #377)

Affected version

0.0.353 Commit: f8fd3e3

Steps to reproduce the behavior

1. Create repo with:

• .github/copilot-instructions.md containing rule: "Always end every answer with [INSTR-OK]."
• agents.md at repo root containing rule: "Always end every answer with [AGENTS-MD-INSTR-OK]."

2. Start copilot-cli in repo root, enter a simple prompt (e.g. "hello").
3. CLI response ends with [INSTR-OK] only.
4. Perform same prompt in VS Code: response ends with [INSTR-OK] [AGENTS-MD-INSTR-OK].

Expected behavior

CLI should merge/apply instructions from both files, matching VS Code behavior.

Additional context

No response

[sergiou87]

I can confirm this difference in behavior between VS Code and Copilot CLI. It seems the agents.md file is ignored when a .github/copilot-instructions.md file exists.

[thawkins]

Even puting a instruction to

"Read the contents of AGENTS.md"

Into copilot-instructions.md does not seem to help.