Add debug logging to copilot permissions, gh-aw-ref resolution, and add command (#56241)

Instruments three pkg/cli files that had no or unused pkg/logger wiring:
copilot-requests permission injection outcomes, --gh-aw-ref resolution,
and the add command's top-level entry/failure points.

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Peli de Halleux <pelikhan@users.noreply.github.com>