Improve test flakes

[cretz]

What was changed

• Added GH timeouts for entire workflow and for specific test runs
• Set macos intel to use 3.13.2 instead of default 3.13 (which is 3.13.3) because the newest released last week was failing, see [Bug] Python 3.13.3 on macOS Intel hangs post-test #834
• Moved all dev servers to v1.3.1-persistence-fix.0 version of CLI dev server to get Pin modernc/sqlite version 1.34.1 cli#784
• macOS on 3.9, like Windows, rarely had a failure exit code post pytest-success, so we enabled same code as Windows to allow it to succeed. We believe this is caused by [Bug] Investigate PyGILState_Release issue for client #300.
• In Python 3.9 still got import errors triggered by CPython bug importlib lock race issue in deadlock handling code python/cpython#91351 when importing pytest into sandbox, so we pass through pytest imports in tests

There are still flakes, such as #300 and some server side persistence failures we are investigating. But this issue solves many common ones for now.