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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