Allow project / GitHub repo addition to recognize bare clones

### Feature summary

_No response_

### What problem are you trying to solve?

When adding a project or GitHub repository, the current flow does not recognize repositories that are bare clones. This makes the repo appear unsupported or unavailable even though it is a valid repository state.

### Proposed solution

Update the repository/project addition flow to detect bare clone repositories and treat them as valid inputs for addition. If there are any limitations, surface a clear message explaining the constraint instead of failing silently or rejecting the repo outright.

### Workflow impact

This would remove a setup blocker for users working with bare clones and make repository onboarding more reliable, especially in environments where repositories are mirrored or managed in bare form.

### Installation context

GitHub App repository addition flow

### Additional context

If relevant, the repository may be managed as a bare clone rather than a working tree checkout.

Start with the GitHub App repository addition flow and trace how it validates repositories without a working tree. Check the bare-clone case first, then define the supported behavior and clear limitation message; done means a bare clone can be added or is rejected with an explicit explanation.

索引モデルが issue の本文から書いたものです。