[codex] Add app behavior shortcuts and tray controls

[spaceshipmike]

Summary

Adds the app behavior and project action shortcut slice on top of the beta branch:

• menu bar persistence with close/minimize-to-hide behavior and explicit real quit handling
• tray menu controls for opening Setlist, Settings, update checks, and quit
• Dock visibility preferences while hidden
• global project-action shortcut registration with validation/status reporting
• project action picker for shortcut targeting
• project detail actions for opening folders, copying the agent brief command, refreshing health, editing, renaming, and archiving
• Settings sections for App behavior and Keyboard commands
• generated Electron app output refresh

Validation

• npm run build -w packages/app
• npm test -- packages/app/src/main/prefs.test.ts packages/app/src/shared/project-actions.test.ts
• npm run test:e2e -w packages/app (passed outside sandbox, 9/9)
• npm run verify:mcp-abi after e2e
• git diff --check

Notes

This targets the beta branch, not main, so the feature can be included in a follow-up beta release such as v0.6.1-beta.2 after review.