fix: refresh Codex skill catalog in place

[nikita-ashihmin]

Summary

• refresh every active session command palette on skills, app-list, and external-config catalog changes
• publish only the newest atomic command snapshot and suppress duplicate updates
• make /skills refresh the structured palette instead of writing the catalog into chat
• negotiate commandPresentation and toolPresentation AIR metadata for skill/plugin commands and app-backed MCP tools
• preserve existing rendering when the client does not opt into the presentation capabilities

Tracks IJAI-884.

Verification

• npm run typecheck
• npm test (544 passed, 26 skipped)
• npm run build