Copilot App forces repository root instead of respecting selected subfolder

### Short summary

When adding a repository, selecting a subfolder is ignored and the app resolves to the repository root.

### Affected version or release

0.2.5

### Installation context

_No response_

### What happened?

**What happened?**

In many monorepo setups, development work is performed within a specific subfolder rather than the repository root. Tooling, instructions, and context are often scoped to that subdirectory.
When adding a repository to the GitHub Copilot App:
- A subfolder is selected during setup
- The app automatically resolves the repository to its root instead
- All sessions are subsequently executed from the root directory

**Expected behavior**

- The app should respect the user-selected subfolder
- Sessions should execute within that folder context
- Instructions, skills, and configuration located in that subfolder should be used

**Actual behavior**

- Selected subfolder is ignored
- Repository is resolved to root
- Sessions run from root instead of the intended subfolder
- Subfolder-specific instructions and configuration are not picked up

**Impact**

- Breaks workflows for monorepo setups
- Prevents effective use of Copilot App in subfolder-based development environments
- Reduces access to relevant instructions and tooling scoped to subdirectories

**Suggested fix**

- Do not automatically resolve to repository root when a subfolder is explicitly selected
- Preserve execution context based on the user-selected path
- Note: T3 Code does this correctly so take a look how it does it

### Steps to reproduce

_No response_

### Expected behavior

_No response_

### Additional context

_No response_