Jax updates for rules_python 1.8.4
1. Update runfile imports and its related python files
2. Add flags to .bazelrc specific for flags used for rules_python
3. Update all .sh runners for ci test to use rules_python_bootstrap except for older python 3.11
4. Fix wheel_build_command to use wheel_build_command_based
5. Make numpy visible
6. Update all the patches for rules_python for scoping and freethreading
PiperOrigin-RevId: 878592042