Sync daily machine-config drift for bebop, frontier, and improv

[Copilot]

Updated mache/cime_machine_config/config_machines.xml to match current
upstream E3SM machine configuration for the supported machines flagged by the
daily drift workflow (bebop, frontier, improv), and aligned impacted
Frontier Spack template package versions for HDF5/NetCDF/PnetCDF drift.

• Description
  • config_machines.xml drift sync
    • Refreshed machine-specific env/module values for:
      • bebop: cmake, hdf5, netcdf, parallel-netcdf related env/path changes
      • frontier: hdf5, netcdf, parallel-netcdf version/module drift
      • improv: parallel-netcdf and LD_LIBRARY_PATH drift
  • Spack template alignment (frontier)
    • Updated package version strings in:
      • frontier_crayamd-mphipcc_mpich.yaml
      • frontier_crayamd_mpich.yaml
      • frontier_craycray-mphipcc_mpich.yaml
      • frontier_craycray_mpich.yaml
      • frontier_craygnu-mphipcc_mpich.yaml
      • frontier_craygnu_mpich.yaml
  • Reviewer TODO handling
    • Added explicit reviewer TODO notes where path/prefix replacements require
      site confirmation instead of guessing.

<env name="PNETCDF_PATH">/path/to/updated/pnetcdf</env>

Checklist

• User's Guide has been updated if needed
• Developer's Guide has been updated if needed
• API documentation lists any new or modified class, method, or function
• Documentation builds cleanly and changes look as expected
• Tests pass and new features are covered by tests
• PR description includes a summary and any relevant issue references
• Testing comment, if appropriate, in the PR documents testing used to verify the changes