Sync config_machines.xml to E3SM a3999e3 for pm-cpu drift

[Copilot]

This updates Mache’s vendored config_machines.xml to match upstream E3SM at
a3999e3d2801a56ebd9bae6fa701372c066c6f1b, addressing the daily drift report
for pm-cpu. The resulting delta is limited to upstream machine-config content.

• Config sync

  • Replaced mache/cime_machine_config/config_machines.xml with the
    generated upstream file from utils/update_cime_machine_config.py.
  • Removed temporary upstream_config_machines.xml after replacement.

• Affected machine delta (pm-cpu)

  • Upstream introduces an additional module load in the relevant block:

<modules compiler="intel">
  <command name="load">PrgEnv-intel/8.6.0</command>
  <command name="load">intel/2025.3</command>
  <command name="load">cray-libsci/25.09.0</command>
</modules>

• Spack template follow-up
  • Reviewed mache/spack/templates/pm-cpu*; no template/version changes were
    indicated by this drift report.

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

[xylar]

Reviewed mache/spack/templates/pm-cpu*; no template/version changes were
indicated by this drift report.

I concur. We were already including cray-libsci/25.09.0 as part of the intel compiler modules in the pm-cpu intel template.