This pull request makes significant improvements to the CI/CD workflows, build configuration, and documentation for the project. The main changes include updating GitHub Actions workflows to use newer versions and more robust caching, switching the Spack repository to a JCSDA fork for dependency management, improving CMake configuration for compiler-specific debug flags and documentation generation, and enhancing library detection and version reporting for SCOTCH. Additionally, new workflows for IO and regression testing with GNU compilers have been introduced.

CI/CD Workflow Updates and Improvements:

• Updated all CI workflows (gnu.yml, intel.yml, and new io_gnu and regtest_gnu workflows) to use actions/checkout@v3 and actions/cache@v3, and switched runners to ubuntu-latest for better compatibility and performance. Enhanced caching strategies and updated cache keys for more robust environment reuse. [1] [2] [3] [4]
• Changed Spack repository from the default to the JCSDA fork in all workflows to ensure consistent dependency management, and added improved Spack environment setup steps. [1] [2] [3] [4]

Build Configuration and Compiler Support:

• Enhanced CMake configuration to set appropriate Fortran debug flags for Intel and IntelLLVM compilers, and added a warning for other compilers. Also introduced the ENABLE_DOCS option for building doxygen documentation. [1] [2]
• Improved Intel workflow setup: updated package installation to specific Intel versions, adjusted compiler environment variables, and refined Spack usage for MPI and compiler requirements. [1] [2]

Documentation Enhancements:

• Added doxygen documentation support in CMake and workflows, including new instructions and configuration for building and outputting docs. Updated the README to link to the generated doxygen documentation. [1] [2] [3] [4]

Library Detection and Reporting:

• Improved FindSCOTCH.cmake to automatically detect and report the SCOTCH library version from headers, making it easier to diagnose build issues and ensure compatibility.

General Maintenance:

• Minor updates to copyright, license, and documentation formatting in README.md.

Let me know if you want to dive deeper into any specific change or workflow!# Pull Request Summary
This PR syncs wavespotter/WW3 fork with updates made to NOAA-EMC/WW3 (in develop branch)

Description

This PR aims to update our WW3 sofar-develop fork (used in our ESM) last updated Apr 19, 2024 (Re-base with NOA-EMC and fix to gustiness) with NOAA-EMC (develop), to coincide with the Sofar-EMC CRADA kick-off (July 9th, 2025). It consists of 86 commits and 283 files changed.

Issue(s) addressed

• Changes to the tail supported (high-frequency) surface stress computation (in ST4).

Commit Message

Check list

• Branch is up to date with the authoritative repository (NOAA-EMC) develop branch.
• Checked the checklist for a developer submitting to develop.
• If a version number update is required, checked the updating version number checklist.
• If a new feature was added, a regression test for testing the new feature is added.

Testing

• How were these changes tested?
• Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
• Have the matrix regression tests been run (if yes, please note HPC and compiler)?
• Please indicate the expected changes in the regression test output, (Note the list of known non-identical tests.)
• Please provide the summary output of matrix.comp (matrix.Diff.txt, matrixCompFull.txt and matrixCompSummary.txt):