The skills_directories configuration entry does not override .github/skills

[dbroeglin]

The skills_directories configuration entry does not override .github/skills

Description

Assuming this directory layout:

And a session configuration that looks like:

    session = await client.create_session(
        {
            "working_directory": "./tests/workspace",
            "skill_directories": ["./tests/workspace/skills"],
        }
    )

When I ask the the agent to enumerate its skills through:

    response = await session.send_and_wait(
        {"prompt": "List all your skills"}
    )

I get the following answer:

I have the following skills available:

| Skill              | Description                                                                                      |
|--------------------|--------------------------------------------------------------------------------------------------|
| `toto`             | A Toto skill.                                                                                    |
| `copilot-sdk-setup`| Guides you through setting up the GitHub Copilot SDK. Supports TypeScript, Python, Go, and .NET. |
| `tutu`             | A Tutu skill.                                                                                    |

Issue

I would expect that skills_directories to override the existing configuration. If it overrides I can always bring back the .github/skills directory as an entry of my configuration. Unless I missed a documentation somewhere, in the current situation, I cannot get rid of .github/skills from the list of directories skills are being loaded from.

[anthonychu]

Global skills in ~/.agents/skills are also being loaded and cannot be overridden, even with enable_config_discovery=False set explicitly.