Site config updates and bug fixes for spack-stack-2.1

[climbfuji]

Is your feature request related to a problem?

For spack-stack-2.1, a few site configs need to be updated to address issues or complete work that didn't make it into spack-stack-2.0.

Describe the solution you'd like

• Hercules: Fix py-scipy build errors (in meson step) with Intel oneAPI compilers - @rickgrubin-noaa and @AlexanderRichert-NOAA @climbfuji
• Orion: Fix py-scipy build errors (in meson step) with Intel oneAPI compilers - @rickgrubin-noaa and @AlexanderRichert-NOAA @climbfuji
• S4: move to tier2, update documentation and release tasklist issue template accordingly - @climbfuji
  • Move S4 and Gaea C5 from tier 1 to tier 2; clean up site config modules.yaml files; bug fix in util/nrl/batch_install.sh #1911
• Gaea C5: Move to tier2, update documentation and release tasklist issue template accordingly - @climbfuji
  • Move S4 and Gaea C5 from tier 1 to tier 2; clean up site config modules.yaml files; bug fix in util/nrl/batch_install.sh #1911
• Derecho: fix GNU build (fix ectrans build errors (in cmake step) with GNU compilers), update oneapi to 2025.3.0 - @climbfuji and @rickgrubin-noaa
  • filesystem.py: prevent recursively traversing the root filesystem spack#576
  • Update Derecho site config #1906
• Narwhal: Thanks to a recent OS update, we now have gcc@13 and cray-mpich@8.1.30 available. Let's try to update to these - @climbfuji
  • Update Narwhal site config, update adp-preprocessors commit #1904
• Containers: Replace current spack ctr builds with a tier 1 site config for a container build that is more similar to how we install on bare-metal systems. @eap with input from EPIC; Clean up as part of this work:
  • Revert spack-stack modifications of container builds in Spack engine code - @climbfuji will be done on develop after the release
  • Remove spack stack ctr extension and associated unit tests - @climbfuji will be done on develop after the release
  • Update documentation and GitHub actions for new container build - @eap will do in the Wiki

Additional context

See discussion (comments) in #1835 for some of the site config build errors encountered during the spack-stack-2.0 release.