Hooks cannot be scoped at a project-specific level in a monorepo

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

Have hooks be able to be scoped at a sub-directory level within a repo, so that projects in a monorepo setup can setup project-specific hooks

### Proposed solution

Currently, a sub-directory .github folder can pick up skills scoped to that directory. This allows monorepo users to setup skills that apply to their project only. Having this apply to hooks will allow monorepo users to utilize hooks functionality as well, which will be a big functionality boost for AI-assisted workflows.

### Example prompts or workflows

- Have a hook that updates an execution plan whenever certain files are updated, so that the execution plan is an accurate source of truth for a given feature, instead of drifting as AI development continues.

### Additional context

This was originally filed as a bug - reclassifying as a feature request after feedback from GH Copilot team: https://github.com/github/copilot-cli/issues/3561

No implementation files or tests are named. Start by reading how sub-directory .github skills are discovered, then trace the existing hook discovery and scoping behavior; done means project-specific hooks work in monorepos without affecting other projects.

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