Update scripts

[schade-shada]

This PR introduces a redesigned scripting system under scripts_2/, replacing the legacy scripts/ workflow for local (vanilla) builds. The new structure separates machine-specific logic from shared common logic, making it straightforward to extend to Levante and other supercomputers in future PRs.

Structure

scripts_2/
├── common/
│   ├── bash/
│   │   ├── build_cleo.sh          # Shared CMake configure step
│   │   ├── compile_cleo.sh        # Shared make/compile step
│   │   └── src/
│   │       ├── build_openmp.sh    # Kokkos OpenMP host flag helper
│   │       ├── build_threads.sh   # Kokkos C++ threads host flag helper
│   │       ├── build_yac.sh       # YAC/YAXT flag helper
│   │       ├── check_inputs.sh    # Input validation utilities
│   │       └── print_configuration.sh
│   └── examples/
│       └── example_params.sh      # Central experiment parameter lookup
└── vanilla/
    ├── build_compile_run_plot_cleo.sh   # Top-level entry point
    └── bash/src/
        ├── build_flags.sh         # Compiler + Kokkos flags (machine-specific)
        └── runtime_settings.sh

Key design decisions

• Separation of concerns: common/ holds logic that is identical across all machines (CMake invocation, compilation, Kokkos parallelism flags). Machine-specific details (compiler selection, MPI paths, runtime settings) live under vanilla/ and will live under levante/, juwels/, etc. in future.
• Consolidated build flags (build_flags.sh): The three previously separate files (build_basic.sh, build_openmp.sh, build_threads.sh) are merged into one machine-specific build_flags.sh. It sets compiler flags and then conditionally applies host-parallelism Kokkos flags based on CLEO_BUILDTYPE (serial / openmp / threads).
• Central experiment registry (example_params.sh): All experiment-specific parameters (build directory, CMake flags, executables, Python script, config file, script arguments) are defined in one place. The top-level script simply passes an experiment name and everything else is resolved automatically.

Future work

• Add scripts_2/levante/ with Levante-specific build_flags.sh, runtime_settings.sh, and SLURM job scripts, reusing all of scripts_2/common/ unchanged.
• Similarly extend to juwels/ and other HPC systems.
• Add a run_cleo.sh wrapper to common/ that invokes the compiled binary directly (currently handled via the Python script's --do_run_executable flag)

Open to suggestions.