fix(run): align script helpers signatures and clarify '--' usage for script flags

- Align make_script_cmakelists and make_script_config_signature signatures
  across run/check script paths
- Fix build errors caused by missing scriptFlags parameter propagation
- Ensure script configuration signature accounts for linker/compiler flags
- Improve CLI UX by documenting the mandatory '--' separator for script flags
  (e.g. vix run main.cpp -- -lssl -lcrypto)