fix: Code quality improvements - format, lint, and type checking fixes

- Replace deprecated datetime.utcnow() with datetime.now(timezone.utc) across 10 files
- Add missing methods to service interfaces (list_sessions_by_entity, store_execution_output_file, kubernetes_manager)
- Fix ExecutionServiceInterface.execute_code signature to return full tuple
- Add None guards for ctx.execution access in orchestrator
- Type ExecutionContext.execution as CodeExecution | None
- Apply ruff formatting across all source files
- Resolve all linter warnings
- Update lockfile with PyPI index