App sees different tools compared to the Copilot CLI

### Short summary

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### Affected version or release

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### Installation context

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### What happened?

I have some project MCPs and skills in my repo, and they work fine when used in Copilot CLI: the CLI finds them and everything works well.

But for some reason, many MCPs and a few skills are missing from the GitHub Copilot App. I tried asking it to fix itself several times, but it is not able to.

Unfortunately I cannot add more details as this is happening in a private company repository.

### Steps to reproduce

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### Expected behavior

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### Additional context

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报告没有列出文件、测试、release、复现步骤或公共仓库的详细信息；它只对比了 Copilot CLI 中的项目 MCPs 和 skills 与 GitHub Copilot App。首先在私有仓库之外收集一个可复现的案例，并比较两个客户端中的工具和 skill 发现情况；当缺失项能够被一致地识别并且在 App 中可用时，即视为完成。

由索引模型根据 Issue 内容生成。