Updates for new deprecation policy

[rjyounes]

• Define predicate gist:isSupersededBy and apply to deprecated terms where relevant.
• Move deprecated terms into gistCore and eliminate gistDeprecated.
• Restore any axioms related to deprecated terms that have been removed.
• Update GitHub documentation accordingly.
  • Add documentation on how to deprecate a term to Contributing.md.
• Update Confluence documentation accordingly.
• Update bundle.yaml.