fix: bump Silo to 4.12.1-pre1, drop patch, fix FFTW CMake 4.x compat

[sbryngelson]

Summary

• Bumps Silo from 4.12.0 to 4.12.1-pre1, which includes the upstream fix for the CMAKE_MODULE_PATH issue (CMakeLists: use list(APPEND) for CMAKE_MODULE_PATH llnl/Silo#550 / Backport sbryngelson fix cmake module path append llnl/Silo#551).
• Removes toolchain/dependencies/Silo.patch and the PATCH_COMMAND stanza — the fix is now upstream.
• Removes the Cray-conditional -DCMAKE_MODULE_PATH=... arg from ExternalProject_Add(silo ...): with list(APPEND CMAKE_MODULE_PATH ...) now in Silo's own CMakeLists.txt, the path injected by MFC's parent cmake is preserved automatically.
• Adds -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to FFTW's ExternalProject_Add so that FFTW 3.3.10 (which declares cmake_minimum_required(VERSION 3.0)) configures correctly under CMake 4.x, which dropped compatibility with VERSION < 3.5.

Closes #1417.

Test plan

• Verify Silo builds cleanly on a Linux CPU build (./mfc.sh build -t post_process)
• Verify Silo build on Frontier (Cray CCE) still works (step 5 from Remove Silo.patch once LLNL/Silo#550 is merged and released #1417)
• Verify FFTW builds correctly under CMake 4.x

[github-actions]

Claude Code Review

Head SHA: e61c2ad

Files changed:

• 2
• toolchain/dependencies/CMakeLists.txt
• toolchain/dependencies/Silo.patch

Findings

[Compiler Portability] Cray-specific CMAKE_MODULE_PATH removed without replacement

The removed line:

"$<$<STREQUAL:${CMAKE_Fortran_COMPILER_ID},Cray>:-DCMAKE_MODULE_PATH=${CMAKE_SOURCE_DIR}/../cmake/cce>"

was the mechanism for injecting Cray-specific find-modules into Silo's ExternalProject sub-build. ExternalProject spawns a fresh CMake process that does not inherit the parent's CMAKE_MODULE_PATH, so this argument was the only way those modules reached the Silo build. The deleted Silo.patch fixed Silo's set(CMAKE_MODULE_PATH …) → list(APPEND …) specifically so that the injected path would survive inside the sub-build.

With both removed, if 4.12.1-pre1 still needs Cray find-modules (e.g., to locate cray-hdf5) the Silo build will fail on Frontier/Carpenter with a cryptic "HDF5 not found" error. The assumption that the new version no longer requires them is not verifiable from the diff alone.

[Reproducibility] Pinning a pre-release tag

GIT_TAG 4.12.1-pre1

Pre-release tags on GitHub can be force-pushed or deleted by the upstream project without notice. GIT_SHALLOW ON still requires the tag to resolve at fetch time; if LLNL removes or moves 4.12.1-pre1 before a stable release is cut, all fresh builds will break. A commit SHA pin alongside the tag would make the build reproducible regardless of upstream tag movement.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 61.31%. Comparing base (3538585) to head (e1396b5).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1442   +/-   ##
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  Coverage   61.31%   61.31%           
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  Files          72       72           
  Lines       19771    19771           
  Branches     2849     2852    +3     
=======================================
  Hits        12123    12123           
  Misses       5699     5699           
  Partials     1949     1949           

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