structure for singularity/containers directory

[espenhgn]

Fixes #284
Fixes #297

Changes proposed in this pull request:

• Removes old SIF files
• Update documentation and code examples accordingly
• Replace Singularity with Apptainer (formerly known as Singularity) throughout documentation.
• Add script <root>/containers/pull_all_containers.py to fetch updated container builds

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  section of the CONTRIBUTING docs.
• I've updated or added any relevant documentation and docstrings where appropriate in the codebase.
• If this PR fixes a bug, I've added a test that will fail without my fix.
• If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.