`.github` folder in a project is not used in the worktree

### Feature summary

Use the `.github` (and private) folders for projects as well

### What problem are you trying to solve?

The session does not take the `.github` or `github-private` folders into account when creating a worktree of a mutli repo project. I created a helpful canvas in a session which I can find in the `.github` repo, yet when I create a new session I cannot use the canvas.

### Proposed solution

Also use the `.github` or `github-private` folders in the worktree.

### Workflow impact

Especially used for multi-repo projects, misses config and functionality right now, including org level Copilot instructions.

### Installation context

_No response_

### Additional context

Local folder setup:

Copilot App:

Worktree:

Start by tracing how a multi-repository session creates its worktree and selects repository folders; check how .github and github-private are handled. Done means those folders are included in the worktree so canvases, configuration, and organization-level Copilot instructions are available in a new session.

Written by the indexing model from the issue text.