--config-dir silently ignores agent files instead of loading them

[cephalin]

Behavior

When using --config-dir to point to a directory containing agent files, the CLI finds the agent (no "No such agent" error) but silently ignores the agent's instructions. The agent's system prompt is not applied.

Steps to reproduce

# 1. Create agent in a custom config dir
mkdir -p /tmp/copilot-test/.github/agents
cat > /tmp/copilot-test/.github/agents/dummy-test.agent.md << 'EOF'
---
description: A dummy test agent
---
You are a dummy test agent. Reply with ONLY: DUMMY_AGENT_OK
EOF

# 2. Run with --config-dir (from a workspace with no agents)
cd /some/empty/workspace
copilot --yolo --config-dir /tmp/copilot-test --agent dummy-test -p "hello"
# Result: "Hello! How can I help?" — agent instructions NOT applied, no error

# 3. Compare: nonexistent agent correctly errors
copilot --yolo --agent nonexistent-xyz -p "hello"
# Result: "No such agent: nonexistent-xyz, available: "

# 4. Compare: same agent in ~/.copilot/agents/ works correctly
mkdir -p ~/.copilot/agents
cp /tmp/copilot-test/.github/agents/dummy-test.agent.md ~/.copilot/agents/
copilot --yolo --agent dummy-test -p "hello"
# Result: "DUMMY_AGENT_OK" — agent instructions applied correctly

Expected behavior

Either:

1. --config-dir should include <config-dir>/.github/agents/ (or <config-dir>/agents/) as an agent discovery path AND load the instructions, or
2. If --config-dir is not intended for agent discovery, the CLI should return "No such agent" instead of silently running without the agent's instructions.

Environment

• copilot CLI installed via Homebrew (/opt/homebrew/bin/copilot)
• macOS
• March 2026

[cephalin]

Additional finding

--config-dir does discover agents from <config-dir>/.github/agents/ — they appear in the "available" list:

copilot --yolo --config-dir /tmp/lu-agent-test --agent nonexistent -p "hello"
# No such agent: nonexistent, available: dummy-test

However, when using a discovered agent, its instructions are silently ignored:

copilot --yolo --config-dir /tmp/lu-agent-test --agent dummy-test -p "Reply DUMMY_AGENT_OK if you are the dummy-test agent"
# Result: "I'm not the dummy-test agent." — instructions not loaded

So the bug is specifically: the CLI indexes agent names from --config-dir but fails to inject their system prompts into the conversation.

[cephalin]

Closing — the original report was based on incorrect testing. --config-dir does work for agent discovery when agents are placed in <config-dir>/agents/ (mirroring ~/.copilot/agents/). The earlier tests incorrectly used <config-dir>/.github/agents/ which is not a valid path for config-dir-based discovery. Apologies for the noise.