Add runtime extra skill roots API (#24977)
## Summary
- Add v2 `skills/extraRoots/set` to replace app-server process-local
standalone skill roots. The setting is not persisted, accepts missing
roots, and `extraRoots: []` clears the runtime set.
- Wire runtime roots into core skill discovery for `skills/list` and
turn loads, clear skill caches on set, and register the roots with the
skills watcher so later filesystem changes emit `skills/changed`.
- Update app-server docs, generated JSON/TypeScript schemas, and
coverage for serialization, missing roots, empty clears, and restart
behavior.
## Testing
- `cargo test -p codex-app-server-protocol`
- `cargo test -p codex-core-skills`
- `cargo test -p codex-app-server
skills_extra_roots_set_updates_process_runtime_roots`
- `just fix -p codex-app-server-protocol`
- `just fix -p codex-core-skills`
- `just fix -p codex-app-server`
xl-openai