The `--config-dir=PATH` is not working as expected

[doggy8088]

Describe the bug

Here is my situation:

1. I have a ~/.copilot/config.json.
2. I run copilot with --config-dir .copilot which I want to set ./.copilot as my primary config directory.

I found that during the execution of Copilot CLI, session data is written to the ./.copilot/ folder, but config.json reads the contents of ~/.copilot/config.json. That's so strange!

Affected version

GitHub Copilot CLI 1.0.9.

Steps to reproduce the behavior

1. Create a ~/.copilot/config.json which assign a model to gpt-5-mini.
2. Create a ./.copilot/config.json which assign a model to claude-sonnet-4.6.

Run copilot --yolo --config-dir .copilot which will load gpt-5-mini model.

Expected behavior

The command arguments should take precedence over and be higher than ~/.copilot/config.json

Additional context

No response

[wang11wang]

The Bug still exists in v1.0.22

[ray-oberg-bankeasy]

I am having the same issue. Here is even a more detailed description of the issue from my experience. I had the CLI make this markdown. This is still in version 1.0.23.

Custom config-dir skills not injected into agent context

Description

When using a custom --config-dir (or equivalent configuration) to define additional skills, the skills appear in the CLI's /skills UI but are not passed to the agent's context. The agent only sees
the built-in skill (customizing-copilot-cloud-agents-environment) and cannot invoke any of the custom-defined skills.

Steps to Reproduce

1. Configure a custom config directory with additional skill definitions (5 total in my case).
2. Launch the CLI with the custom config-dir.
3. Run /skills — all 5 skills are listed in the UI.
4. Ask the agent to use one of the custom skills (e.g., "use skill ado-pipeline-migration").
5. The agent reports it can only see 1 skill (customizing-copilot-cloud-agents-environment).
6. The skill invocation fails with: Skill not found: ado-pipeline-migration.

Expected Behavior

All skills defined in the custom config-dir should be injected into the agent's <available_skills> context so the agent can discover and invoke them.

Actual Behavior

• The /skills command in the CLI UI correctly shows all 5 custom skills.
• The agent's system context only contains 1 built-in skill.
• Attempting to invoke a custom skill results in Skill not found.
• Switching models (e.g., Claude Sonnet 4.6 → Claude Opus 4.6) does not resolve the issue.
• Restarting the session does not resolve the issue.

Environment

• OS: Windows
• CLI Version: (run /version to fill in)
• Shell: PowerShell
• Custom config-dir: Yes (with 5 skill definitions)

Additional Context

The disconnect appears to be between the CLI's skill registry (which correctly reads the custom config-dir) and the agent's system prompt injection (which only includes built-in skills). The skills are
visible at the UI layer but are not propagated to the <available_skills> block in the agent's context.