Add runtime extra skill roots API

[xl-openai]

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