skillDirectories Does Not Take Effect at Repo Level

### Describe the feature or problem you'd like to solve

Working with skills spread across multiple repos or in subdirectories of mono-repos are currently not possible to include without a lot of copying around and cleaning up.

### Proposed solution

Support `skillDirectories` setting both in `.github/copilot/settings.json` and `.github/copilot/settings.local.json` so that we can customise which skills are exposed based on the type of work, the sub-path in a mono-repo and when working across multiple repos. All three scenarios are fairly common in a medium to large enterprise.

### Example prompts or workflows

Let's say I'm working on a frontend-repo and I notice that the backend is not adhering to the contract. I'd like from my frontend-repo to invoke the following skill that lives in backend-repo:
`/investigate-backlog to see if there's a bug on data path of controller Foo where it returns a string instead of a guid`

It wouldn't make sense for me to have it in my user settings since it's dependent upon the type of work I'm doing and the repo I'm currently using. If I duplicate the skill in frontend-repo's .github folder, then I can't be sure when backend folks update something on their end and I get outdated results.

### Additional context

A bit similar to the following issues but not the same IMO:
- #3688
- #3505

Start by tracing how skillDirectories is currently read from user settings and how repository settings are loaded. Compare the behavior of .github/copilot/settings.json and .github/copilot/settings.local.json, including skills in other repositories and monorepo subdirectories. Done means both repository-level files can customize the exposed skill directories without copying skills.

Written by the indexing model from the issue text.